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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 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 %.
Orthopoxviruses are large DNA viruses that replicate within the cytoplasm of infected cells encoding over a hundred different proteins. The orthopoxviral 68k ankyrin‐like protein (68k‐ank) is highly conserved among orthopoxviruses, and this study aimed at elucidating the function of 68k‐ank. The 68k‐ank protein is composed of four ankyrin repeats (ANK) and an F‐box‐like domain; both motifs are known proteinprotein interaction domains. The F‐box is found in cellular F‐box proteins (FBP), crucial components of cellular E3 ubiquitin (Ub) ligases. With yeast‐two‐hybrid screens and subsequent co‐immunoprecipitation analyses, it was possible to identify S‐phase kinase‐associated protein 1a (Skp1a) as a cellular counterpart of 68k‐ank via binding to the F‐box‐like domain. Additionally, Cullin‐1 was co‐precipitated, suggesting the formation of a viral‐cellular SCF E3 Ub ligase complex. Modified Vaccinia virus Ankara (MVA) ‐ being attenuated and unable to replicate in most mammalian cell lines due to a block in morphogenesis – nevertheless, expresses its complete genetic information attributing to its properties as promising vector vaccine. Conservation of 68k‐ank as the only ANK protein encoded by MVA implied a substantial role of this viral factor. Hence, its function in the viral life cycle was assessed by studying a 68k‐ank knock‐out MVA. A mutant phenotype manifested in nonpermissive mammalian cells characterized by a block succeeding viral early gene expression and by a reduced ability of the virus to shutoff host protein synthesis. Studies with MVA encoding a 68k‐ank F‐box‐like domain truncated protein revealed that viral‐cellular SCF complex formation and maintenance of viral gene expression are two distinct, unrelated functions fulfilled by 68k‐ank. Moreover, K1, a well‐described VACV host range factor of the ANK protein family, is able to complement 68k‐ank function. This suggests that gene expression of MVA putatively depends on the ANKs encoded in 68k‐ank. In addition to the important findings in vitro, first virulence studies with the mouse pox agent, ectromelia virus (ECTV) deleted of the 68k‐ank ortholog (C11) suggested that this factor contributes to ECTV virulence in vivo.
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.
By adopting a variety of shapes, proteins can perform a wide number of functions in the cell, from being structural elements or enabling communication with the environment to performing complex enzymatic reactions needed to sustain metabolism. The number of proteins in the cell is limited by the number of genes encoding them. However, several mechanisms exist to increase the overall number of protein functions. One of them are post-translational modifications, i.e. covalent attachment of various molecules onto proteins. Ubiquitin was the first protein to be found to modify other proteins, and, faithful to its evocative name, it is involved in nearly all the activities of a cell. Ubiquitylation of proteins was believed for a long time only to be responsible for proteasomal degradation of modified proteins. However, with the discovery of various types of ubiquitylation, such as mono-, multiple- or poly-ubiquitylation, new functions of this post-translational modification emerged. Mono-ubiquitylation has been implicated in endocytosis, chromatin remodelling and DNA repair, while poly-ubiquitylation influences the half-life of proteins or modulates signal transduction pathways. DNA damage repair and tolerance are example of pathways extensively regulated by ubiquitylation. PCNA, a protein involved in nearly all types of DNA transaction, can undergo both mono- and poly-ubiquitylation. These modifications are believed to change the spectrum of proteins that interact with PCNA. Monoubiquitylation of PCNA is induced by stalling of replication forks when replicative polymerases (pols) encounter an obstacle, such as DNA damage or tight DNA-protein complexes. It is believed that monoubiquitylation of PCNA stimulates the exchange between replicative pols to one of polymerases that can synthesize DNA across various lesions, a mechanism of damage tolerance known as translesion synthesis (TLS). Our work has helped to understand why monoubiqutylation of PCNA favours this polymerase switch. We have identified two novel domains with the ability to bind Ub non-covalently. These domains are present in all the members of Y polymerases performing TLS, and were named Ub-binding zinc finger (UBZ) (in polη and polκ) and Ub-binding motif (UBM) (in polι and Rev1). We have shown that these domains enable Y polymerases to preferentially gain access to PCNA upon stalling of replication, when the action of translesion polymerases is required. While the region of direct interaction between Y pols and PCNA had been known (BRCT domain in Rev1 and PIP box motif (PIP) in three others members), we propose that Ub-binding domains (UBDs) in translesion Y pols enhance the PIP- or BRCT-domain-mediated interaction between these polymerases and PCNA by binding to the Ub moiety attached onto PCNA. Following these initial studies, we have also discovered that Y polymerases themselves undergo monoubiquitylation and that their UBDs mediate this modification. This auto-ubiquitylation is believed to lead to an intramolecular interaction between UBD and Ub attached in cis onto the UBD-containing protein. We have mapped monoubiquitylation sites in polη in the C-terminal portion of the protein containing the nuclear localization signal (NLS) and the PIP box. Beside PIP, the NLS motif is also involved in direct interaction of polη with PCNA. Based on these findings, we propose that monoubiquitylation of either NLS or PIP masks them from potential interaction with PCNA. Lastly, using several functional assays, we have demonstrated the importance of all these three motifs in the C-terminus of polη (UBZ, NLS and PIP) for efficient TLS. We have also constructed a mimic of monoubiquitylated polη by genetically fusing polη with Ub. Interestingly, this chimera is deficient in TLS as compared to the wild-type protein. Altogether, these studies demonstrate that the C-terminus of polη constitutes a regulatory module involved in multiple-site interaction with monoubiquitylated PCNA, and that monoubiquitylation of this region inhibits the interaction between polη and PCNA. Our work has also revealed that the UBDs of Y pols as well as of other proteins implicated in DNA damage repair and tolerance, such as the Werner helicase-interacting protein 1 (Wrnip1), are required for their proper sub-nuclear localization. All these proteins localize to discrete focal structures inside the nucleus and mutation of their UBDs results in inability to accumulate in these foci. Interestingly, by exchanging UBDs between different proteins we have learned that each UBD seems to have a distinct functional role, surprisingly not limited to Ubbinding ability. In fact, swapping the UBZ of Wrnip1 with the UBM of polι abolished the localization of Wrnip1 to foci despite preserving the Ub-binding ability of the chimeric protein. In summary, this work provides an overview of how post-translation modification of proteins by Ub can regulate several DNA transactions. Firstly, key regulators (e.g. PCNA) can be differentially modified by Ub. Secondly, specialized UBDs (e.g. UBM, UBZ) embedded only in a subset of proteins act as modules able to recognize these modifications. Thirdly, by means of mediating auto-ubiquitylation, UBDs can modulate the behaviour of host proteins by allowing for either in cis or in trans Ub-UBD interactions.
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).
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.
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.
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.
Large amplitude intramolecular motions in non-rigid molecules are a fundamental issue in chemistry and biology. The conventional approaches for study these motions by far-infrared and microwave spectroscopy are not applicable when the molecule is non-polar. Therefore, in the current thesis an alternative approach for the investigation of large amplitude intramolecular motions was developed and tested. This new method is based on femtosecond rotational degenerate four-wave mixing spectroscopy (fs DFWM), which is a particular implementation of rotational coherence spectroscopy. The method was successfully applied for the investigation of pseudorotation in pyrrolidine and the ring-puckering vibration in cyclopentene. Another important subject is the photophysics of molecules and molecular clusters which have an ultrashort lifetime of their electronically excited state (photoreactivity). These ultrashort lifetimes often represent a protective mechanism causing photostability. The photoreactivity is usually the manifestation either of an “elementary” reaction, such as proton or electron transfer, which occurs in the excited state or of a fast non-radiative deactivation processes, such as internal conversion via conical intersection of the electronically excited and ground state. Due to a short-lived excited state, the conventional vibrational spectroscopic methods, such as IR depletion detected by resonance two-photon ionization spectroscopy (IR/R2PI), are not applicable for the structural investigation of these systems. Therefore, new approach, termed IR depletion detected by multiphoton ionization with femtosecond laser pulses (IR/fsMPI), was developed for studying the structure of photoreactive microsolvated molecules. The IR/fsMPI technique was applied for investigating the clusters of 1H-pyrrolo[3,2-h]quinoline with water/methanol as well as adenine- and 9-methyl-adenine-hydrates. In addition, the excited state dynamics of bifunctional azaaromatic molecule 7-(2'-pyridyl)indole (7PyIn) was studied by femtosecond pump-probe resonance excitation multiphoton ionization technique (fs REMPI). Under electronic excitation of this molecule a fast proton transfer (phototautomerization) takes place, which is followed by radiationless excited state deactivation process. The fs REMPI spectra lead to the conclusion that the phototautomerization in 7PyIn is coupled with a twisting of the molecule, and that the twisting provides an efficient channel for ultrafast radiationless excited state deactivation. This pattern of excited-state tautomerization/deactivation might be quite general.
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. ...
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.
Dendritic cells are the sentinels between the innate and the adaptive immunity. They are professionals that capture invading pathogens, recognize specific microbial structures and induce naïve T lymphocytes to polarize into a specific T cell subset. To initiate the T cell polarization DCs secrete cytokines which are induced upon Toll-like receptor activation by microbial structures. The recognition of these structures and the discrimination between non-self and self structures by TLRs is fine tuned, but under defined circumstances deregulation of immune responses appears. Consequently, this can result in immune disorders such as autoimmunity, chronic inflammatory diseases or cancer. In this thesis the investigations are focused on the regulation of the IL-12 family members IL-12p70 and IL-23 in DCs. The objective was to investigate three different endogenous and exogenous factors that regulate IL-12p70 or IL-23. In the first part Selenium, an essential trace element and important factor in several metabolic pathways including the cellular redox status and reactive oxygen species (ROS) dependent signaling was applied as supplement in immature Langerhans cell culture. Because Selenium also plays a role in the immune system the TLR-induced IL-23 production of the DCs upon Selenium treatment was analyzed. In the immature Langerhans cell line XS-52 the strongest inducer of IL-23 was TLR4 ligand LPS. Furthermore increased levels of TLR4-induced IL-23 in cells treated with Selenium were detected in a concentration dependent manner. Whereas the IL-23 subunit p40 was upregulated upon Selenium treatment the second subunit p19 was completely unaffected. This effect was detected on mRNA and protein level. In addition, as expected, IFN-gamma inhibited the TLR4-induced IL-23 secretion of both, Selenium treated and untreated cells. In the second part of this thesis p47phox, an organizing protein of the NADPH oxidase was analyzed regarding its potential to regulate IL-12p70 and/or IL-23 secreted by different DC subtypes. Since it was demonstrated that p47phox deficiency is associated with enhanced autoimmunity and chronic inflammation we wanted to prove whether it has a function in addition to that within the NADPH oxidase. We found some hints that p47phox may be interact with proteins of the TLR signaling pathway and thus we hypothesized that p47phox may have a function for the regulation of TLR-mediated cytokine production in DCs. In several experiments with DCs from the spleen of different p47phox deficient mice we detected an increased production of TLR9-induced IL-12p70 compared to wild type cells. In contrast TLR4 stimulation with LPS displayed no significant differences between p47phox deficient and wild type cells. In spleen cells IL-23 was not detected. Confirming the results of this new negative feedback by p47phox on IL-12p70 rats, with a single nucleotide polymorphism in the p47phox gene, were investigated. Interestingly this polymorphism is located in the phosphorylation site of IRAK4, an important kinase in the TLR pathway. In rats with a methionine residue at this position in the p47phox protein enhanced IL-12p70 level were found, compared to the rats with threonine, which can be phosphorylated by IRAK4. All analyzed mice and rats have defects in the NADPH oxidase function due to a non functional p47phox protein which results in a defective ROS production. To determine whether the observed negative feedback mechanism is connected to the lack of ROS production experiments with gp91phox deficient mice, which also have a defective NADPH oxidase function, were performed. In several experiments the enhanced IL-12p70 production in cells from p47phox deficient mice could be confirmed, but no differences between gp91phox deficient and wild type mice have been observed. In further studies was found that the inhibition of the NADPH oxidase function did not alter the negative feedback on TLR9-induced IL-12p70 secretion by p47phox. Interestingly upon treatment with the inhibitor a feedback mechanism in wild type cells also after TLR4 stimulation was observed. Hence, blocking a ROS-dependent TLR4 pathway by the inhibitor uncovered the LPS induced ROS-independent pathway of the TLR4 signaling. These findings strongly approve a NADPH oxidase/ROS-independent function of p47phox in DCs. Because splenic DCs do not secrete IL-23, in vitro differentiated DCs from the bone marrow were investigated regarding the negative feedback mechanism. In DCs from p47phox deficient mice, differentiated with GM-CSF, the upregulation of IL-12p70 was confirmed, whereas Flt3-L cultured DCs did not display the negative feedback. In contrast to IL-12p70 no difference for the IL-23 production between wild type and p47phox deficient cells has been detected. Thus, we concluded that IL-23 production is not regulated by p47phox. IL-12p70 is the major cytokine in the Th1 polarization whereas IL-23 is important for the maintenance and survival of Th17 cells. To prove whether the regulation of IL-12p70 influences the T cell response immunization experiments closely resembling the classical DTH-like protocols were performed. Groups of p47phox deficient and wild type mice received either PBS, OVA alone or mixed with TLR9 ligand CpG2216 in IFA s.c. to activate and polarize naïve T cells towards Th1 or Th17 cells. After ten days isolated lymph node cells were incubated in an ELISA spot assay with or without OVA and the frequency of IFN-gamma and IL-17 producing T cells was quantified. In vitro recall of OVA immunization of wild type and p47phox deficient mice resulted in an increased IFN-gamma and IL-17 frequency in the p47phox deficient cells. The combination with CpG2216 as adjuvant and inducer of the 3rd signal enhanced the frequency of IFN-gamma and IL-17 producing T cells in wild type mice significantly. However, in p47phox deficient cells the IFN-gamma and IL-17 response, being already detectable without in vitro OVA re-stimulation, was strongly augmented upon OVA restimulation. These findings confirmed our in vitro data for IL-12p70. Hence, the data supports our hypothesis that the p47phox dependent regulation of IL-12p70 and the consequences for the T cell response is an important mechanism to prevent uncontrolled immune responses. In the last part of this thesis the immunomodulatory property of vitamin D3 on the IL-12p70 production of DCs was examined. Since it was shown that VD3 influences the differentiation and maturation of monocytes and DCs, splenic DCs from C57BL/6 and BALB/c mice were investigated regarding their IL-12p70 production after VD3 treatment. Spleen cells, stimulated with LPS or CpG2216, exhibited a decreased IL-12p70 production when treated with VD3 before stimulation phase. In contrast treatment with VD3 only during TLR stimulation had no influence on the IL-12p70 production. Since it was demonstrated that VD3 stimulates the expression of p47phox mRNA cells from p47phox deficient mice were also treated with VD3. In initial experiments only a slight inhibition of IL-12p70 has been detected in p47phox deficient cells compared to the wild type. In summary the thesis displays three different possibilities to influence the TLR-induced cytokine secretion of DCs, although with different intensities and specificities.
Through the use of information about the biological target structure, the optimization of potential drugs can be improved. In this work I have developed a procedure that uses the quantitative change in the chemical perturbations (CSP) in the protein from NMR experiments for driving protein-ligand docking. The approach is based on a hybrid scoring function (QCSPScore) which combines traditional DrugScore potentials, which describe the interaction between protein and ligand, with Kendall’s rank correlation coefficient, which evaluates docking poses in terms of their agreement with experimental CSP. Prediction of the CSP for a specific ligand pose is done efficiently with an empirical model, taking into account only ring current effects. QCSPScore has been implemented in the AutoDock software package. Compared to previous methods, this approach shows that the use of rank correlation coefficient is robust to outliers. In addition, the prediction of native-like complex geometries improved because the CSP are already being used during the docking process, and not only in a post-filtering setting for generated docking poses. Since the experimental information is guaranteed to be quantitatively used, CSP effectively contribute to align the ligand in the binding pocket. The first step in the development of QCSPScore was the analysis of 70 protein-ligand complexes for which reference CSP were computed. The success rate in the docking increased from 71% without involvement of CSP to 100% if CSP were considered at the highest weighting scheme. In a second step QCSPScore was used in re-docking three test cases, for which reference experimental CSP data was available. Without CSP, i.e. in the use of conventional DrugScore potentials, none of the three test cases could be successfully re-docked. The integration of CSP with the same weighting factor as described above resulted in all three cases successfully re-docked. For two of the three complexes, native-like solutions were only produced if CSP were considered.Conformational changes in the binding pockets of up to 2 Å RMSD did not affect the success of the docking. QCSPScore will be particularly interesting in difficult protein-ligand complexes. They are in particular those cases in which the shape of the binding pocket does not provide sufficient steric restraints such as in flat protein-protein interfaces and in the virtual screening of small chemical fragments.
This thesis presents a 5.9 Å map of yeast FAS obtained by cryo-electron microscopy using single particle analysis (SPA). The EM-map has been analyzed both by quantitative and qualitative analysis to aid in understanding of the structure and dynamics of yeast FAS. This study approaches the factors limiting the resolution in EM (>20 Å) and further discusses the possibilities of achieving higher-resolutions (<10 Å) in cryo-EM by single particle analysis. Here, SPA is highlighted as a powerful tool for understanding the structure and dynamics of macro-molecular complexes at near native conditions. Though SPA has been used over the last four decades, the low-resolution range (20-30 Å) of the method has limited its use in structural biology. Over the last decade, sub nanometer resolution (<10 Å) structures solved by SPA have been reported --both in studies involving symmetric particles, such as GroEL (D7) and asymmetric particles, such as ribosomes (C1). Recently, near-atomic resolution in the range of 3.8-4.2 Å has been achieved in cases of highly symmetric icosahedral viral capsid structures as well. The yeast FAS structure (D3) presented here is one of two low symmetry structures submitted to the EM-database in a resolution range of 5-6 Å; the other being GroEL (D7). Fatty acid synthase (FAS) is the key enzyme for the biosynthesis of fatty acids in living organisms. There are two types of FAS, namely the type II FAS system in prokaryotes, consisting of a set of individual enzymes, and type I FAS found in eukaryotes as a multienzyme complex. Yeast fatty acid synthase (FAS) is a 2.6 MDa barrel-shaped multienzyme complex, which carries out cyclic synthesis of fatty acids. By electron cryomicroscopy of single particles we obtained a 3D map of yeast FAS at 5.9 Å resolution. Compared to the crystal structures of fungal FAS, the EM map reveals major differences and new features that indicate a considerably different arrangement of the complex in solution, as well as a high degree of variance inside the barrel. Distinct density regions in the reaction chambers next to each of the catalytic domains fit well with the substratebinding acyl carrier protein (ACP) domain. In each case, this resulted in the expected distance of ~18 Å from the ACP substrate binding site to the active site of the catalytic domains. The multiple, partially occupied positions of the ACP within the reaction chamber provide direct insight into the proposed substrate-shuttling mechanism of fatty acid synthesis in this large cellular machine.
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.
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.
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.
Delthyridoid spiriferids are characterized by a global abundance and fast evolution during Silurian and Devonian, and, therefore, are used as important biostratigraphical and palaeobiogeographical tools. In this work, delthyridoid brachiopod faunas from different regions of today’s world, resp., of different palaeobiogeographical units, are compared side-by-side to investigate their phylogenetic relationships and to improve, in a second step, the palaeobiogeography from Late Silurian to Early Eifelian time. A new systematics of Delthyridoidae is established which is more complicated than hitherto assumed. The results of this study are mainly based on direct comparison of articulated and isolated brachiopod shells, external and internal moulds, as well as latex casts and serial sections. The computer supported cladistic analyses have turned out not to be useful due to different kinds of preservation resulting in an incomplete matrix which is insufficient for reliable cladograms. A further problem in terms of cladistical analyses are various convergences during the evolution of spiriferids. Many characters evolved independently from each other at different times in each lineage so that autapomorphies are hardly or not at all recognizable. As a result, families and genera are only definable by a combination of characters rather than by a single or a few autapomorphies. As a new method, 3D reconstruction from serial sections is introduced which made it possible for the first time to compare directly mouldic and shelly material. Preliminary results are presented herein. Statistical analyses of measurements taken from new taxa are made but regarded as a descriptive argument rather than a deciding factor for taxonmy due to incomplete preservation and/or tectonic deformation. Brachiopods, especially type material, from collections of different institutions and museums are studied as well as personal material, whenever possible collected from topotype outcrops. Emended diagnoses, if necessary, from family to species level are given. During this work several new taxa have been erected: 7 new families: Australospiriferidae, Murchisonispiriferidae, Orientospiriferidae, Otospiriferidae, Patriaspiriferidae, Rostrospiriferidae, and Trigonospiriferidae; 6 new genera, 1 of these in open nomenclature: Cyclopterospirifer, Hallispirifer, Parlinispirifer, Murchisonispirifer, Shujiapingensispirifer, and gen. nov. B; and 3 new species: Patriaspirifer merriami, Patriaspirifer johnsoni, and Murchisonispirifer feldmani; 1 taxon is defined as nomen novum: Orientospirifer nakaolingensis wani. In the framework of this project, 2 families: Filispiriferidae and Multispiriferidae; 1 subfamily: Multiplicatispiriferinae, 6 genera, 1 of them in open nomenclature: Frequentispirifer, Leonispirifer, Multiplicatispirifer, Ovetensispirifer, Turcispirifer, and Gen. A; and 9 new species, 3 of them in open nomenclature: Filispirifer hamadae, Leonispirifer leonensis, Multiplicatispirifer foumzguidensis, Oventensispirifer novascotianus, Quiringites arensentiae, Turcispirifer turciae, Multiplicatispirifer cf. foumzguidensis, Quiringites cf. arensentiae, and ?Turcispirifer sp. A which have already been established are also described in this work. The brachiopod faunas studied consist of externally very similar spiriferids which have been identified as same genera, species, or even subspecies in earlier times. These forms are considered as 6 distinct morphotypes Howellella-, Arduspirifer-, Acrospirifer-, Euryspirifer-, Paraspirifer-, and Multiplicatispirifer-like morphotypes, which are briefly introduced. The new systematics is characterized by different clades, the European/North African delthyridoid spiriferid clade, the North American delthyridoid spiriferid clade, the Asian delthyridoid spiriferid clade, the Malvinokaffric delthyridoid spiriferid clade, and the delthyridoid multiplicated spiriferid clade. Each of them is described in a cladistic and in a phylogenetic way. Their phylogenetic relationship sheds new light on palaeobiogeographical interpretations for the different stages from Late Silurian to early Middle Devonian time. A tendency for increasing endemicity is seen until the end of the Early Emsian, which is interrupted by short term regional faunal exchange within a province or within a realm, followed by a loss of endemicity resulting in global distribution of brachiopod genera until the end of Givetian time. The Old World Realm is re-defined due to the lack of phylogenetic relationship between its faunas and subdivided into the European Realm, consisting of the Gondwanan and Avalonian provinces, and the Asian Realm, consisting of the Siberian, Sino, and Mongolian provinces. A reconstruction of Lower Devonian palaeobiographical map is introduced.
TeaABC from the halophilic bacterium Halomonas elongata belongs to the family of tripartite ATP-independent periplasmic (TRAP) transporters. It facilitates the uptake of the compatible solutes ectoine and hydroxyectoine which protect the cell from dehydration by accumulating in the cytoplasm during hyperosmotic stress. It is the only known TRAP transporter activated by osmotic stress. Ectoine and hydroxyectoine accumulation in H. elongata is regulated by the cytoplasmic universal stress protein TeaD. The gene encoding TeaD is located in the same operon as the TeaABC gene. TeaD regulates the cellular homeostasis of ectoine possibly by interacting directly or indirectly with TeaABC. All subunits of TeaABC and TeaD were expressed in E. coli and purified. With TeaD and the solute binding protein (SBP) TeaA high levels of expression suitable for crystallization could be obtained and their 3D structures solved. The small transmembrane protein TeaB and the transporter TeaC showed only moderate and low levels of expression respectively. Functional analysis on TeaA was performed using Isothermal Titration Calorimetry. The measurements demonstrate that TeaA is a high affinity ectoine-binding protein (Kd = 0.19 _M) that also has a significant affinity for hydroxyectoine (Kd = 3.8 _M). The structure of TeaA was solved using ab initio phase determination by MAD (multiple anomalous dispersion). TeaA structures were determined in three conformations: TeaA alone, TeaA in complex with ectoine and TeaA in complex with hydroxyectoine. The resolutions of the structures were 2.2, 1.55 and 1.80 Å, respectively. These represent the first structures of an osmolyte SBP associated to a TRAP transporter. The structures reveal similar ligand binding compared to osmolyte SBPs of ABC transporter pointing to coevolution of the ligand binding modes. Moreover, unique features such as the solvent-mediated specific binding of the ligands ectoine and hydroxyectoine could be observed for TeaA. The structure of TeaD in complex with its cofactor ATP was solved by molecular replacement at a resolution of 1.9 Å. Comparison with other structures of universal stress proteins shows striking oligomerization and ATP binding in TeaD. In conclusion, this work presents the first detailed analysis of the molecular mechanisms underlying ligand recognition of an osmoregulated transporter from the TRAP-transporter family.
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.
Der zentrale Aspekt der vorliegenden Arbeit ist die Untersuchung psychophysiologischer Konsequenzen von Emotionsregulationsanforderungen und deren Beeinflussung durch individuelle Differenzen. Hierbei wurden in Studie 1 subjektive, verhaltensbezogene und physiologische Konsequenzen von Emotionsregulation und deren Beeinflussung durch individuelle Differenzen untersucht. Die Studien 2, 3 und 4 fokussieren auf Emotionsregulation in einem Service-Kontext (Emotionsarbeit). Während in der Emotionsregulationsforschung der Einfluss individueller Differenzen bisher wenig untersucht wurde, existieren insbesondere in der Emotionsarbeitsforschung kaum experimentelle Studien, die kausale Rückschlüsse auf den Zusammenhang von emotionalen Regulationsanforderungen mit subjektiven, verhaltensbezogenen und physiologischen Reaktionen erlauben. Hierbei fanden insbesondere physiologische Parameter und individuelle Differenzen keine bzw. wenig Berücksichtigung. Studie 1 zeigte, dass individuelle Differenzen eine moderierende Wirkung auf den Zusammenhang von Emotionsregulationsinstruktionen und verhaltensbezogenen sowie physiologischen Reaktionen aufweisen. In den Studien 2 und 3 konnte gezeigt werden, dass die Vorgabe, emotionale Zustände darzustellen, die nicht in der Arbeitssituation empfunden werden (emotionale Dissonanz), in einer simulierten Interaktion mit einem unzufriedenen Kunden mit mehr Emotionsregulation und mit einer verstärkten physiologischen Belastung des Service-Angestellten einherging. Ebenso waren in den Studien 2, 3 und 4 Versuchsteilnehmer mit einer geringen negativen Affektivität (hier: Trait-Ärger bzw. Neurotizismus) durch geringere psychophysiologische Belastungsreaktionen gekennzeichnet, sofern starke Regulationsanforderungen an sie gestellt wurden. Zudem zeigte sich in Studie 4, dass die Vorgabe, positive emotionale Zustände 40 darzustellen, zu einer organisational vorteilhafteren Expressionsleistung gegenüber der Vorgabe negative emotionale Zustände nicht zu zeigen, führte. Zusammenfassend sprechen diese Ergebnisse dafür, dass häufige Konfrontationen mit starken Regulationsanforderungen die Belastung von Service-Angestellten erhöhen und die Entwicklung von kardiovaskulären Erkrankungen begünstigen können. Die vorliegenden Moderatoreffekte implizieren, dass Personen mit geringer negativer Affektivität weniger vulnerabel gegenüber den negativen Konsequenzen starker emotionaler Regulationsanforderungen in unangenehmen Kundeninteraktionen sind.
Quantum entanglement plays a basic role in quantum information science. The creation of entanglement between qubits is of fundamental importance for further computation processing like quantum computation, quantum cryptography, quantum teleportation, quantum computers… We present here a symmetric electron-electron scattering experiment to determine the experimental parameters which are necessary to produce a source of entangled electrons. In this Moeller scattering experiment the electrons differ from each other only by their spin direction. At these conditions a spin entanglement of the scattered electrons is expected. To demonstrate the spin entanglement, a single particle resolved spin measurement of the electrons has to be performed. A high ratio of measured coincidences compare to random could be demonstrated. It is shown, that this ratio is related to an experiment depended nearly constant efficiency for the coincidence detection. In order to proof the spin entanglement, the goal is to measure the final polarization state of the electrons at different scattering directions to observe a spin anti correlation between these spin states of the Moeller electrons. The usual method to determine the electron polarization is based on an asymmetric scattering experiment with a high Z target. This scattering may yield an asymmetry due to a different spin-orbit coupling of the electrons. The main problem of polarized electron studies at keV-particle energy is the low efficiency of usual spin polarimeters. This low efficiency impedes or prevents electron spin resolved coincidence measurements because of necessarily induced random coincidences. To enhance the efficiency of the spin detection, a new compact mini-Mott spin analyzer has been developed. Due to a compact small size of this analyzer, a higher efficiency is obtained now, which is a prerequisite to the electron spin resolved coincidence measurements. Till date, the asymmetry measurement have been performed where one Mott analyzer rotated by an angle around the axis. The reducing asymmetry is in agreement with a prediction of quantum mechanic; however, the large systematic errors of the measurement have been estimated. As a next step for investigation of spin entanglement it is planned to increase the overall efficiency of the experiment by having higher initial energy and minimize error of the measurement by applying new kind of detectors.
Energy and environment are two major concerns in the 21st century. At present, the energy required for the daily life still mainly relies on the traditional fossil fuel resources, but the caused air pollution problem and greenhouse effect have seriously threatened the sustainable development of mankind. Another adopted energy source which can provide a large fraction of electricity for the world is the nuclear fission reaction. However, the increasing high-radioactive spent nuclear fuels, which half-lives are usually >1 million years, are becoming the hidden perils to the earth. A great advance in accelerator physics and technology opens an opportunity to solve this dilemma between man and nature, because powerful accelerator-based neutron sources can play important roles for clean nuclear power production, for example: - The Accelerator-Driven System (ADS) can serve as an easy control of a sub-critical fission reactor so that the nuclear fuels will be burnt more completely and safely. - The EUROTRANS project launched by EU is investigating another application of the ADS technology to reduce the radiotoxicity and the volume of the existing nuclear waste greatly and quickly in a transmutation way. - The developing international IFMIF plant will be used to test and qualify reactor materials for future fusion power stations, which can produce much cleaner nuclear electricity more efficiently than the fission ones. Therefore, the R&D of high-power driver linacs (HPDL) is of a worldwide importance. As the proverb said, "everything is hard at the beginning", the front end is the most difficult part for realizing an HPDL machine. Based on the RFQ and H-type DTL structures, this dissertation is dedicated to study the beam dynamics in the presence of significantly strong space-charge effects while accelerating intense hardon beams in the low- and medium-beta-region. Besides the 5mA/30mA, 17MeV proton injector (RFQ+DTL) and the 125mA, 40MeV deuteron DTL of the above-mentioned EUROTRANS and IFMIF facilities, a 200mA, 700keV proton RFQ has been also intensively studied for a small-scale but ultra-intense neutron source FRANZ planned at Frankfurt University. The most remarkable properties of the FRANZ RFQ and the IFMIF DTL are the design beam intensities, 200mA and 125mA, which are the record values for the proton and deuteron linacs, respectively. Though the design intensities for the two development stages, XT-ADS (5mA) and EFIT (30mA), of the EUROTRANS injector are well within the capability of the modern RF linac technology, the special design concept for an easy upgrade from XT-ADS to EFIT brings unusual challenges to realize a linac layout which allows flexible operation with different beam intensities. To design the 200mA FRANZ RFQ and the two-intensity EUROTRANS RFQ, the classic LANL (Los Alamos National Laboratory) Four-Section Procedure, which was developed by neglecting the space-charge forces, is not sufficient anymore. Abandoning the unreasonable constant- B (constant-transverse-focusing-strength) law and the resulting inefficient evolution manners of dynamics parameters adopted by the LANL method, a new design approach so-called "BABBLE", which can provide a "Balanced and Accelerated Beam Bunching at Low Energy", has been developed for intense beams. Being consistent with the beam-development process including space-charge effects, the main features of the "BABBLE" strategy (see Pages 55-58) are: 1) At the entrance, the synchronous phase is kept at = phi s = -90° while a gradual increase in the electrode modulation is started so that the input beam can firstly get a symmetrical and soft bunching within a full-360° phase acceptance. 2) In the following main bunching section, B is increasing to balance the stronger and stronger transverse defocusing effects induced by the decreasing bunch size so that the bunching speed can be fast and safely increased. 3) When the real acceleration starts, the quickly increased beam velocity will naturally weaken the transverse defocusing effects, so B is accordingly falling down to avoid longitudinal emittance growths and to allow larger bore apertures. Taking advantage of the gentle initial bunching and the accelerated main bunching under balanced forces enabled by the "BABBLE" strategy, a 2m-long RFQ with beam transmission in excess of 98% and low emittance growths has been designed for FRANZ, and a 4.3m-long RFQ with almost no beam losses and flat emittance evolutions at both 5mA and 30mA has been designed for EUROTRANS. All design results have proven that the "BABBLE" strategy is a general design approach leading to an efficient and robust RFQ with good beam quality in a wide intensity-range from 0mA to 200mA (even higher). To design the IFMIF DTL and the injector DTL part of the EUROTRANS driver linac, which have been foreseen as the first real applications of the novel superconducting CH-DTL structure, intensive attempts have been made to fulfill the design goals under the new conditions, e.g. long drift spaces, SC transverse focusing elements and high accelerating gradients. For the IFMIF DTL, the preliminary IAP design has been considerably improved with respect to the linac layout as well as the beam dynamics. By reserving sufficient drift spaces for the cryosystem, diagnostic devices, tuner and steerer, introducing SC solenoid lenses and adjusting the Linac Design for Intense Hadron Beams accelerating gradients and accordingly other configurations of the cavities (see Pages 78-80), a more realistic, reliable and efficient linac system has been designed. On the other hand, the specifications and positions of the transverse focusing elements (see Pages 81-82) as well as the phase- and energy-differences between the bunch-center particle and the synchronous particle at the beginning of the phi s=0° sections have been totally redesigned (see Pages 83-84) resulting in good beam performances in both radial and longitudinal planes. For the EUROTRANS injector DTL, in addition to the above-mentioned procedures, extra optimization concepts to coordinate the beam dynamics between two intensities, such as employing short adjustable rebunching cavities with phi s = -90° (see Page 116), have been applied. ...
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.
The transporter associated with antigen processing-like (TAPL) acts as a lysosomal ATP-dependent polypeptide transporter with broad length selectivity. To characterize in detail its substrate specificity, a procedure for solubilization, purification and functional reconstitution of human TAPL was developed. TAPL was expressed in Sf9 insect cells with the baculovirus expression system and solubilized from crude membranes. By intensive screening of detergents, the mild non-ionic detergents digitonin and dodecylmaltoside were found to be ideal for solubilization with respect to efficiency, long term stability, and functionality of TAPL. TAPL was isolated in a two-step procedure with a yield of 500 micro g/L cell culture and, subsequently, reconstituted into proteoliposomes. The KM(pep) for the peptide RRYCfKSTEL (f refers to fluorescence label) and KM(ATP) were determined to be 10.5 ± 2.3 micro M and 97.6 ± 27.5 micro M, respectively, which are in the same range as the Michaelis-Menten constants determined in the membranes. The peptide transport activity of the reconstituted TAPL strongly depends on the lipid composition. Interestingly, the E. coli lipids are prefered over other tested natural lipids extracts. Moreover, phosphatidylcholine, the most abundant phospholipid in eukaryotic cells influenced TAPL activity in a dose dependent manner. In addition, some negatively charged lipids like DOPA and DOPS increased peptide transport activity with preference for DOPS. However, DOPE or egg PG which are also negatively charged had no effect. It seems not only the charge but also the specific head group of phospholipids that has impact on the function of TAPL. With the help of combinatorial peptide libraries containing D-amino acid residues at defined positions as well as bulky fluorescein labeled peptides, the key positions of the peptides were localized to the N- and C-terminal residues with respect to peptide transport. The C-terminal position has the strongest selectivity since modification at this position shows strongest impact on peptide transport. Additionally, positions 2 and 3 of the peptide also have weak influence on peptide selectivity. Subsequently, the residue preferences at the key positions were systematically investigated by combinatorial peptide libraries with defined residues at certain positions. At both ends, TAPL favors positively charged, aromatic, or hydrophobic residues and disfavors negatively charged residues as well as asparagine and methionine. The residue preferences at the key positions are valid for peptide substrates with different length, indicating a general rule for TAPL selectivity. Besides specific interactions of both terminal residues, electrostatic interactions are important, since peptides with positive net charge are more efficiently transported than negatively charged ones. By size exclusion chromatography (SEC) and blue native PAGE, TAPL purified in the presence of digitonin or dodecylmaltoside had an apparent molecular weight of 200 kDa which is close to the theoretical molecular mass of the TAPL homodimer (172 kDa). The purified and reconstituted TAPL showed specific ATP hydrolysis activity which can be inhibited by orthovanadate. TAPL in proteoliposomes showed 6-fold higher ATP hydrolysis than digitonin solubilized protein, indicating the phospholipids impact on TAPL function. However, no peptide substrate stimulated ATPase activity was observed. For site-specific labeling of TAPL, eight cysteines in each half transporter were replaced by alanine or valine. The TAPL cys-less mutant showed the same peptide transport activity as TAPL wt. Based on the functional TAPL cys-less mutant, seven single cysteine mutants were introduced into strategic positions. All single cysteine mutants in the TMD did not influence peptide transport, whereas the mutant L701C, which is close to the conserved H-loop motif, displayed impaired transport. TAPL orthologs Haf-4 and Haf-9 from Caenorhabditis elegans possess around 40% sequence identities with TAPL and 50% with each other. Both proteins are putative half transporters and reported to be involved in the intestinal granule formation (Bauer, 2006; Kawai et al., 2009). To further understand the physiological functions of these two proteins, they were expressed in Sf9 insect cells. Haf-4 and Haf-9 showed weak but specific ATP- and peptide-dependent peptide transport activity for the given peptide RRYCfKSTEL. Therefore, it was proposed that the physiological roles for Haf-4 and Haf-9 might be related to their peptide transport activity. Besides forming functional homodimeric complex as estimated by the peptide transport activities, both half transporter could also form heteromers which was confirmed by coimmunoprecipitation. However, the heteromers showed decreased transport activity.
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.
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.
Very little is known about the occlusal wear pattern in the Neanderthal posterior dentition. Usually dental wear is closely related to the physical properties of the ingested food, and consequently can be used to obtain information about diet. Neanderthal dietary reconstructions have been mostly based on the analysis of accompanying faunal remains and isotopic signatures of bones and tooth enamel, suggesting that they exploited larger portions of animal proteins from large and medium-sized herbivores. Probably these studies may do not reflect the bulk diet, tending to underestimate plant consumption and to overestimate meat consumption. In the present work the occlusal wear pattern of maxillary molars of Homo neanderthalensis (N=19) and early Homo sapiens (N=12)have been analyzed, applying non-destructive methods based on virtual three-dimensional polygonal models generated from surface scanning of dental casts. The sample groups occupied different geographical areas at different chronological times. The 3D digital tooth models were analyzed using the “Occlusal Fingerprint Analysis” (OFA) method (Kullmer et al. 2009), describing and quantifying the occlusal wear pattern derived from two wear facet angles (dip and dip direction), wear facet area and occlusal relief index (ORI). The OFA method provides information about the dynamics of the occlusal relationships and their function, permitting the reconstruction of the mandibular movements responsible for the contacts created during the chewing cycle. Since jaw movements and diet are closely related, the results obtained, can be used to interpret the diet of the two Pleistocene hominin species. In order to evaluate how dietary differences influence the occlusal wear pattern, upper molars of modern hunter-gatherers (N=42) with known diet and different dietary habits, have been included in the sample and compared with those of Neanderthals and early Homo sapiens. Results show that within the modern hunter-gatherers sample, the occlusal wear pattern of carnivorous populations differs from those who relied on a mixed-diet. In particular, the study of relative facet areas clearly distinguish meat-eaters from mixed-diet hunter-gatherers, while ORI results and wear facet inclinations (dip angle) seem to reflect directly the abrasiveness of the diet, including the influence of exogenous materials during food preparation. The Neanderthal occlusal wear pattern is characterized by an ecogeographic variation, suggesting the exploitation of different food resources. In particular Neanderthals who inhabited relatively warm environments of southern Europe and the Near East exhibit an occlusal wear pattern different from those of meat-eaters hunter-gatherers from tempered and cooler regions, displaying some features similar to those of Bushmen. These results suggest the exploitation of a broad variety of food sources. The analysis of the occlusal wear pattern in Neanderthals and early Homo sapiens who inhabited Europe during the cooler Oxygen Isotope Stage 3 (OIS3) shows many similarities between the two hominid species. These results indicate the exploitation of similar and low-diversified food sources, based mostly on the consumption of animal proteins, as suggested through the clear similarities with the wear patterns found in modern meat-eaters hunter-gatherers. In both studied groups, Neanderthals and early Homo sapiens the occlusal wear pattern is characterized by high ORI and dip angle values, suggesting the intake of a low-abrasive diet, probably due to the absence of sophisticated food preparation techniques introducing external silica grains, e.g. from soil (grinding of seeds) or plant cells, as those, seen in modern hunter-gatherer populations. The analysis of the occlusal fingerprints in Neanderthal and early European Homo sapiens upper molars suggests that both species followed very similar adaptive dietary strategies, based on a distinctive versatility and flexibility in the daily diet, depending on availability of resources according to environmental circumstances.
We investigate the utility of modern kernel-based machine learning methods for ligand-based virtual screening. In particular, we introduce a new graph kernel based on iterative graph similarity and optimal assignments, apply kernel principle component analysis to projection error-based novelty detection, and discover a new selective agonist of the peroxisome proliferator-activated receptor gamma using Gaussian process regression. Virtual screening, the computational ranking of compounds with respect to a predicted property, is a cheminformatics problem relevant to the hit generation phase of drug development. Its ligand-based variant relies on the similarity principle, which states that (structurally) similar compounds tend to have similar properties. We describe the kernel-based machine learning approach to ligand-based virtual screening; in this, we stress the role of molecular representations, including the (dis)similarity measures defined on them, investigate effects in high-dimensional chemical descriptor spaces and their consequences for similarity-based approaches, review literature recommendations on retrospective virtual screening, and present an example workflow. Graph kernels are formal similarity measures that are defined directly on graphs, such as the annotated molecular structure graph, and correspond to inner products. We review graph kernels, in particular those based on random walks, subgraphs, and optimal vertex assignments. Combining the latter with an iterative graph similarity scheme, we develop the iterative similarity optimal assignment graph kernel, give an iterative algorithm for its computation, prove convergence of the algorithm and the uniqueness of the solution, and provide an upper bound on the number of iterations necessary to achieve a desired precision. In a retrospective virtual screening study, our kernel consistently improved performance over chemical descriptors as well as other optimal assignment graph kernels. Chemical data sets often lie on manifolds of lower dimensionality than the embedding chemical descriptor space. Dimensionality reduction methods try to identify these manifolds, effectively providing descriptive models of the data. For spectral methods based on kernel principle component analysis, the projection error is a quantitative measure of how well new samples are described by such models. This can be used for the identification of compounds structurally dissimilar to the training samples, leading to projection error-based novelty detection for virtual screening using only positive samples. We provide proof of principle by using principle component analysis to learn the concept of fatty acids. The peroxisome proliferator-activated receptor (PPAR) is a nuclear transcription factor that regulates lipid and glucose metabolism, playing a crucial role in the development of type 2 diabetes and dyslipidemia. We establish a Gaussian process regression model for PPAR gamma agonists using a combination of chemical descriptors and the iterative similarity optimal assignment kernel via multiple kernel learning. Screening of a vendor library and subsequent testing of 15 selected compounds in a cell-based transactivation assay resulted in 4 active compounds. One compound, a natural product with cyclobutane scaffold, is a full selective PPAR gamma agonist (EC50 = 10 +/- 0.2 muM, inactive on PPAR alpha and PPAR beta/delta at 10 muM). The study delivered a novel PPAR gamma agonist, de-orphanized a natural bioactive product, and, hints at the natural product origins of pharmacophore patterns in synthetic ligands.
Solid state NMR is a emerging method for the study of membrane proteins, which has received much interest in recent years. Limiting the study of many pharmacologically relevant targets, are the often long measuring times, required to obtain especially higher dimensional solid state NMR spectra of good quality. To address this problem, multiple methods where developed in this work, which can be categorized into two groups. The first set of methods aims at the quality of certain spectra, by implementing a spectral filter, which increases the fidelity of the measured data. The second set of methods, addresses the problem of long measuring times directly, by increasing the sensitivity per unit time, as could be shown, for example, on homo- and heteronuclear singlequantum-singlequantum correlation experiments. The gains in measuring time for the latter group of methods are typically in the order of 2-3, but some experiments allow multiple methods to be employed simultaneously, which can lead to a decrease in measuring time of a factor of up to 8. It is important to mention, that none of the methods introduced in this work require any equipment in addition to the conventional setup present in most sold state NMR laboratories and no changes or addition to the samples under study are required. Therefore the gains reported in this work come at no extra cost and require only minimal implementation effort on the side of the user.
The peroxisome proliferator activated receptor gamma (PPARgamma) plays an eminent role during alternative activation of macrophages and resolution of inflammation. As an antiinflammatory signaling molecule, it seems likely that it is tightly regulated dependent on the state of the immune response. There is growing evidence that PPARgamma expression is reduced during inflammation, whereas molecular mechanisms are illdefined. Even though, its role in immunosuppression is getting more definite. Apoptotic cells (AC) provoke an active repression of pro-inflammatory responses inter alia by the inhibition of pro-inflammatory cytokine expression or attenuated generation of reactive oxygen species (ROS). The reduced formation of ROS was attributed to PPARgamma activation, while mechanisms behind the reduced cytokine expression remained unclear. Therefore, my Ph.D. thesis addressed the role of PPARgamma during inhibited cytokine synthesis in response to AC and the regulation of PPARgamma expression during an inflammatory response, which was initiated by lipopolysaccharide (LPS) exposure. In the first part of the thesis, I investigated the role of PPARgamma in coordinating the attenuation of pro-inflammatory cytokine expression in response to AC. Exposing murine RAW264.7 macrophages to AC prior to LPS-stimulation, reduced NFKB transactivation and lowered target gene expression of e.g. TNFalpha and IL-6 compared to controls. In macrophages over-expressing a dominant negative (d/n) mutant of PPARgamma, NFKB transactivation in response to LPS was restored, while using macrophages from myeloid lineage-specific conditional PPARgamma knock-out mice proved that PPARgamma transmitted the anti-inflammatory response delivered by AC. Domain analysis revealed that amino acids 32-250 are essential for inhibition of NFKB. Mutation of a SUMOylation (SUMO: small-ubiquitin related modifier) site in this region (K77R) and interfering SUMOylation by silencing the SUMO E3 ligase PIAS1 (protein inhibitor of activated Stat1) eliminated AC-provoked NFKB inhibition and concomitant TNFalpha expression. Chromatin-immunoprecipitation assays demonstrated that AC prevented the LPS-induced removal of nuclear receptor co-repressor (NCoR) from the KB response element within the TNFalpha promoter. I concluded that AC induce PPARgamma SUMOylation to attenuate the removal of NCoR, thereby blocking transactivation of NFKB. This contributes to an anti-inflammatory phenotype shift in macrophages in response to AC, by lowering pro-inflammatory cytokine production. The second part addressed molecular mechanisms responsible for reduced PPARgamma expression upon LPS exposure. PPARgamma gained considerable interest as a therapeutic target during chronic inflammatory diseases. Remarkably, the pathogenesis of diseases such as multiple sclerosis or Alzheimer’s disease is associated with impaired PPARgamma expression. Initiation of an inflammatory response by exposing primary human macrophages to LPS revealed a rapid decline of PPARgamma1 expression. PPARgamma1 mRNA decrease was prevented by inhibition of NFKB and also after pre-treatment with the PPARgamma agonist rosiglitazone, suggesting a NFKB-dependent pathway, because activated PPARgamma is known to inhibit NFKB transactivation. Since promoter activities were not affected by LPS, I focused on mRNA stability and noticed a decreased PPARgamma1 mRNA half-life. RNA stability is often regulated via 3’ untranslated regions (UTRs). Therefore, I analyzed the impact of the PPARgamma-3’UTR by luciferase assays. LPS significantly reduced luciferase activity of pGL3-PPARgamma-3’UTR, suggesting that PPARgamma1 mRNA is destabilized. Deletion of a potential miR-27a/b binding site within the 3’UTR completely restored luciferase activity. Moreover, inhibition of miR-27b, which was induced upon LPS-exposure, partially reversed PPARgamma1 mRNA decay, whereas the mature miR-27 mimicked the effect of LPS. MiR-27b was at least partially induced by NFKB, thus correlating with NFKB-dependent PPARgamma1 mRNA decrease. Since deletion of the miR-27 site also containing an AU-rich element (ARE) completely abrogated LPS-induced reduction but inhibition of miR-27b only partially restored PPARgamma1 mRNA expression, I suggested an additional implication of an ARE-binding protein. I provide evidence that LPS induces miR-27b, which in turn destabilizes PPARgamma1 mRNA. Understanding the molecular mechanism of PPARgamma mRNA destabilization, might help to rationalize inflammatory diseases associated with impaired PPARgamma expression. Even though, further experiments are needed to clarify the potential involvement of ARE-binding proteins.
It has been shown that stem and progenitor cells are therapeutically effective after i.v application. Yet, many aspects regarding intracellular signaling pathways which are involved in the homing and local action of these cells still have to be elucidated. In this work, it was aimed to investigate the role of the small GTPase Rap1 in adhesion activation in Hematopoietic Stem and Progenitor Cells (HSC/HPC) and in Mesenchymal Stem Cells (MSC). The potential role of Rap1 was assessed in, mice which were homozygote negative for the expression of the Rap1a gene. Peripheral blood lymphocyte counts as well as numbers of HPCs in the blood were decreased in Rap1a-/- mice compared to wild-type controls. Additionally the adhesion capability of HPCs from Rap1a-/- to the endothelial ligand, Vascular Cell Adhesion Molecule – 1 under shear stress was decreased. The hematopoietic repopulation potential of Rap1a-/- HPC was however not decreased in a competitive bone marrow transplantation model, indicating that deficiency of Rap1a in HSC/HPC does not negatively affect their ability to interact with the bone marrow microenvironment. In contrast, the isolation of MSC was not possible from Rap1a-/- bone marrow, indicating an altered situation in the bone marrow niche through changed stromal cell behaviour. Instead, Rap1a+/- MSC could be isolated and showed an adhesion deficit under shear stress. In contrast, no differences were noted in their differentiation potential. In a mouse homing model, the overall ability of the Rap1a+/- MSC to home to different tissues was found preserved. Finally, in a murine subcutaneous carcinoma model, cells with an HPC phenotype were observed to be present in the tumor microenvironment, and it was shown that they home directly to tumors. Since HPC isolated from bone marrow were able to differentiate into cells with a pro-angiogenic phenotype in vitro, HPC may be of relevance for neovascularization, as tumor-infiltrating progenitor cells. The results of the study should contribute to the understanding of the regulation of progenitor cell homing behaviour in situations simulating cell therapy approaches in preclinical situations.
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.
Plant parasitic species of Asterinaceae and Microthyriaceae (Dothideomycetes, Ascomycota, Fungi) are inconspicuous foliicolous fungi with a mainly tropical distribution. They form black colonies on the surface of living leaves. Members of Asterinaceae and Microthyriaceae are characterized by shield-shaped, flat ascomata (thyriothecia) which grow completely superficially on the leaf cuticle. Microthyriaceae, Asterinaceae and other families of thyriothecia-forming ascomycetes belong to the class Dothideomycetes due to the presence of bitunicate asci. However, until today no consistent taxonomic concept nor molecular phylogenetic studies exist for the families of thyriothecioid ascomycetes. In the present thesis, 42 species belonging to 13 different anamorphic and teleomorphic genera of Asterinaceae, Microthyriaceae and ‘Pycnothyriales’ recently collected in Western Panama, are identified, described in detail and illustrated with drawings, transmission and scanning electron microscopical photographs. Among the 42 species, 37 species belong to the Asterinaceae, four species to the Microthyriaceae and one species to the from group ‘Pycnothyriales’. Two species of Asterinaceae are new to sience: Asterina gaiadendricola with an Asterostomella anamorph and Asterina schlegeliae with a Mahanteshamyces anamorph. Among the remaining species of Asterinaceae, 28 species represent new records for Panama: Asterina cestricola, A. ciferriana, A. consobrina, A. corallopoda, A. davillae with anamorph, A. diplocarpa, A. diplopoda, A. ekmanii, A. fuchsiae, A. manihotis, A. phenacis, A. radiofissilis with anamorph, A. siphocampyli, A. sponiae, A. stipitipodia with anamorph, A. styracina, A. tonduzii with anamorph, A. weinmanniae, A. zanthoxyli, Asterostomella dilleniicola, Asterolibertia licaniicola, Asterolibertia nodulosa, Cirsosia splendida with its Homalopeltis chrysobalani anamorph and Prillieuxina winteriana with its Leprieurina winteriana anamorph. The remaining 11 species of Asterinaceae probably respresent new species: Asterina spp. 1-8, Asterolibertia sp., Halbanina sp. and Mahanteshamyces sp. The four species of Microthyriaceae are new records for Panama: Maublanica uleana, Platypeltella irregularis, Platypeltella smilacis and Xenostomella tovarensis. The species Hemisphaeropsis magnoliae in the form group ‘Pycnothyriales’ is a new record for Panama. During this study, voucher material of 44 additional species of plant parasitic thyriothecioid ascomycetes was examined. Thereby, the number of species of Asterinaceae known for Panama since 2006 raises from four to 30, for Microthyriaceae respectively from zero to four and for ‘Pycnothyriales’ from zero to one. 21 of the presented species are new records for Central America and two species are new records for the American Continent. The presented 42 species parasitize 47 host plant species in 39 genera belonging to 28 plant families. For 23 fungal species, new host plant species are discovered. From those, seven belong to host plant genera not reported before to be parasitized by a member of Asterinaceae and Microthyriaceae: Burmeistera (Campanulaceae), Curatella and Davilla (Dilleniaceae), Greigia (Bromeliaceae), Hirtella (Chrysobalanaceae), Oxandra and Xylopia (Annonaceae). In this study, the first molecular phylogenetic approach in Asterinaceae is provided. For the first time, DNA was isolated from fresh material of Asterina spp. and their respective anamorphic stages on leaves in Panama. The hypothesis derived from SSU and LSU rDNA neighbour-joining analysis supports the monophyly of the Asterinaceae and suggests a close relationship to Venturiaceae within the class Dothideomycetes. The data obtained from the ppMP project (plant parasitic microfungi of Panama) indicate a constant but low abundance of plant parasitic thyriothecioid ascomycetes in natural plant communities in Panama, with Asterinaceae as the most species-rich and diverse family. Further collection activities in tropical regions worldwide will certainly increase our knowledge about species diversity and ecology of tropical plant parasitic thyriothecioid ascomycetes.
Sepsis is caused by infection and often followed by an overwhelming inflammatory response. This can lead to shock, organ failure and even death. Each year approximately 60,000 people die in Germany due to sepsis. There is good evidence that sepsis is associated with failure of the hypothalamic-pituitary-adrenal-axis. In patients with sepsis, glucocorticoids (e.g. corticosterone, cortisol) released from adrenal glands play an essential role in preventing an excessive pro-inflammatory response. Adrenal insufficiency occurs in a large number of patients with septic shock and is associated with an increased mortality. In the innate immune system, Toll-like receptors (TLRs) play a crucial role in its onset by recognizing pathogenassociated molecules. It is well known that there are interactions between the immune and endocrine stress systems; glucocorticoids and TLRs regulate each other in a bi-directional way. Therefore, a coordinated response of the adrenal and immune system is of vital importance for survival during severe inflammation. This experimental study focuses on the role of TLR-2, TLR-4 and TLR-9 during adrenal stress. The results show that in mice, the absence of TLR-2 and TLR-4, but not TLR-9 leads to altered adrenal morphology, relating to size and cellular structure. However, this alteration does not appear to compromise the phenotype of TLR knock-out mice. Mice deficient of TLR-2, 4 and 9 are not able to respond adequately to inflammatory stress induced by their potential ligands lipopolysaccharide (LPS), lipoteichoic acid (LTA) or cytidine phosphate guanosine-oligodeoxynucleotides (CpG-ODN). This impaired adrenal stress response appears to be associated with a decrease in systemic and intra-adrenal cytokine expressions. Taken together, these results suggest that TLR-2, 4 and 9 are key players in the immuno-endocrine response during inflammation and SIRS. In conclusion, TLRs play a crucial role in the immune-adrenal crosstalk. This close functional relationship needs to be considered in the treatment of inflammatory diseases where an intact adrenal stress response is required. Furthermore, TLR polymorphisms could contribute to the underlying mechanisms of impaired adrenal stress response in patients with bacterial sepsis
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.
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.
In over 100 genera of tropical angiosperms, one or more species possess specialised structures for housing ants. The longevity and intimacy of these associations has often facilitated an increasing specialisation of both the ants and the plants, leading to a number of highly specific and obligate symbioses. Early literature contained only few anecdotal reports of the ant genus Cladomyrma WHEELER inhabiting (unidentified) plants. This work presents the new findings on Cladomyrma and its host plants that accumulated over the last two decades. My studies of Cladomyrma reveal that there is a largely overlooked community of south-east Asian plant-ants and their associated plants. Currently the genus consists of at least 12 species. Cladomyrma has been thought to be restricted to the ever-wet part of the West Malesian floristic region, comprising the Malay Peninsula, Borneo, and Sumatra, but recent collections from Thailand and Vietnam indicate that species of the genus penetrate the seasonal tropical forests of Continental Asia. Cladomyrma inhabits 24 plant species belonging to a surprisingly extensive range of plant taxa: Callerya, Saraca, Spatholobus (Fabaceae), Crypteronia (Crypteroniaceae), Drypetes (Putranjivaceae), Ryparosa (Achariaceae), Strychnos (Loganiaceae), Neonauclea (Rubiaceae), Luvunga (Rutaceae) and Sphenodesme (Verbenaceae). In terms of taxonomic diversity on the genus and family level the range of hosts utilised by Cladomyrma is one of the broadest ever recorded for any live stem-nesting plant-ant lineage worldwide. This work provides a species-level overview of all Cladomyrma host plants known from Borneo, the Malay Peninsula and Sumatra, including descriptions of ant-housing structures (domatia), ant inhabitant identity, onset of colonisation during plant ontogeny, nest structure, occupancy rate, and considerations of results obtained from herbarium specimens. Both the regularity of ant association and the degree of morphological specialisation toward myrmecophytism are assessed. The behavioural traits of Cladomyrma are compatible with traits exhibited by other protective plant-ants. This work demonstrates that all species of Cladomyrma investigated (dianeae, maschwitzi, yongi, petalae) confer antiherbivore protection to young leaves of its host. The ants also attack and repell or kill herbivorous insect larvae encountered on young foliage. Cleaning behaviour appears to be a trait shared by all members of the genus, and the two species tested (maschwitzi, petalae) successfully removed termite eggs experimentally placed onto young leaves. Another trait common to all known species of the genus is that the ants preferentially patrol young shoots and leaves ('neophily'). These behavioural traits of Cladomyrma likely reduce stem damage and pathogenic infection of their host. The ants prune encroaching vegetation (tested in dianeae maschwitzi, petalae, yongi, observed in crypteroniae) and attack paper tape used to mark host plants (observed in andrei, dianeae, hobbyi, nudidorsalis, maschwitzi, yongi, petalae). If these traits combined translate into a better reproductive success of the hosts has yet to be verified. Evidence for lifetime fitness benefits is particularly difficult to quantify for the long-lived woody host plants of Cladomyrma. The predominant food source of Cladomyrma appears to be the honeydew of scale insects (Coccidae and Pseudococcidae) which the ants tend inside their nest cavities. Observations on scale insect acquisition by Cladomyrma foundress queens show that hemipteran trophobionts are not transported by the queens on their nuptial flight but they nevertheless arrive on the host plant independently of the ants. Entry into nest chambers is facilitated by small holes kept open by the foundress queen. Most Cladomyrma species have been recorded from only one or two (three) host plant species (andrei, crypteroniae, hobbyi, maschwitzi, nudidorsalis, scopulosa, yongi), but two species, Cladomyrma petalae and C. dianeae, are more catholic in their host usage; the first being a 'generalist' plant-ant colonising hosts across a broad taxonomic range, the second inhabiting several members of the genus Neonauclea. First results of host-choice experiments with C. petalae are presented and the potential mechanisms promoting host specificity are discussed. My studies of the Cladomyrma/plant associations indicate that codiversification and host shifts or host expansions, rather than cospeciation, shape the pattern of species interactions in this system. Finally, I propose a scenario in which three key traits of Cladomyrma –access to live stems, utilisation of indirect food rewards via trophobionts and 'neophily'– are hypothesised to favour niche differentiation and the acquisition of new hosts over evolutionary time.
Tropical geometry is the geometry of the tropical semiring \[\mathbb{T}:=(\mathbb{R}\cup\{\infty\},\min,+).\] Classical algebraic structures correspond to tropical structures. If $I\lhd K[x_1,\ldots,x_n]$ is an ideal in a polynomial ring over a field $K$ with valuation $v$, then the classical algebraic variety correspond to the tropical variety $T(I)$. It is the set of all points $w$, such that the minimum $\min\{v(c_\alpha)+w\cdot\alpha\}$ is achieved twice for all $f=\sum_\alpha c_\alpha x^\alpha\in I$. So tropical geometry relates algebraic geometric problems with discrete geometric problems. In this thesis we obtain a tropical version of the Eisenbud-Evans Theorem which states that every algebraic variety in $\mathbb{R}^n$ is the intersection of $n$ hypersurfaces. We find out that in the tropical setting every tropical variety $T(I)$ can be written as an intersection of only $(n+1)$ tropical hypersurfaces. So we get a finite generating system of $I$ such that the corresponding tropical hypersurfaces intersect to the tropical variety, a so-called tropical basis. Let $I \lhd K[x_1,\ldots,x_n]$ be a prime ideal generated by the polynomials $f_1, \ldots, f_r$. Then there exist $g_0,\ldots,g_{n} \in I$ such that \[ T(I) \ = \ \bigcap_{i=0}^{n}T(g_i)\] and thus $\mathcal{G} := \{f_1, \ldots, f_r, g_0, \ldots, g_{n}\}$ is a tropical basis for $I$ of cardinality $r+n+1$. Tropical bases are discussed by Bogart, Jensen, Speyer, Sturmfels and Thomas where it is shown that tropical bases of linear polynomials of a linear ideal have to be very large. We do not restrict the tropical basis to consist of linear polynomials and therefore we get a shorter tropical basis. But the degrees of our polynomials can be very large. The main ingredient to get a short tropical basis is the use of projections, in particular geometrically regular projections. Together with the fact that preimages of projections of tropical varieties are themselves tropical varieties of a certain elimination ideal we get the desired result. Let $I \lhd K[x_1, \ldots, x_n]$ be an $m$-dimensional prime ideal and $\pi : \mathbb{R}^n \to \mathbb{R}^{m+1}$ be a rational projection. Then $\pi^{-1}(\pi(T(I)))$ is a tropical variety, namely \[ \pi^{-1}(\pi(T(I))) \ = \ T(J \cap K[x_1, \ldots, x_n]) \,\] Here $J$ is an ideal in $K[x_1,\ldots,x_n,\lambda_1,\ldots,\lambda_{n-m-1}]$ derived from the ideal $I$. We show that this elimination ideal is a principal ideal which yields a polynomial in our tropical basis. The advantage of our method is that we find our polynomials by projections and therefore we can use the results of Gelfand, Kapranov and Zelevinsky , of Esterov and Khovanskii , and of Sturmfels, Tevelev and Yu. With mixed fiber polytopes we get the structure and combinatorics of the image of a tropical variety and therefore the structure of the polynomials in our tropical basis. Let $I=\lhd K[x_1,\ldots,x_n]$ an $m$-dimensional ideal, generated by generic polynomials $f_1,\ldots, f_{n-m}$, $\pi:\mathbb{R}^n\to\mathbb{R}^{m+1}$ a projection and $\psi$ a projection presented by a matrix with a rowspace equal to the kernel of $\pi$. Then up to affine isomorphisms, the cells of the dual subdivision of $\pi^{-1} \pi T(I)$ are of the form \[ \sum_{i=1}^p \Sigma_{\psi} (C_{i1}^{\vee}, \ldots, C_{i{k}}^{\vee}) \] for some $p\in\mathbb{N}$ and faces $F_1, \ldots, F_p$ of $T(f_1)\cap\ldots\cap T(f_k)$ and the dual cell of $F_i\subseteq U = T(f_1)\cup\ldots\cup T(f_k)$ is given by $F_i^\vee=C_{i1}^{\vee}+ \ldots+ C_{ik}^{\vee}$ with faces $C_{i1}, \ldots, C_{i k}$ of $T(f_1), \ldots, T(f_{k})$. In case that we project a tropical curve we want to find the number of $(n-1)$-cells of the above form with $p>1$, i.e. the cells which are dual to vertices of $\pi(T(I))$ which are the intersection of the images of two non-adjacent $1$-cells of $T(I)$. Vertices of this type are called selfintersection points. We show that there exist a tropcal line $L_n\subset\mathbb{R}^n$ and a projection $\pi:\mathbb{R}^n\to\mathbb{R}^2$, such that $L_n$ has $\sum_{i=1}^{n-2}i$ selfintersection points. Furthermore we find tropical curves $\mathcal{C}\subset\mathbb{R}^n$, which are transversal intersections of $n-1$ tropical hypersurfaces of degrees $d_1,\ldots,d_{n-1}$ and a projection $\pi:\mathbb{R}^n\to\mathbb{R}^2$, such that $\mathcal{C}$ has at least $(d_1\cdot\ldots\cdot d_{n-1})^2\cdot \sum_{i=1}^{n-2}i) $ selfintersection points. A caterpillar is a certain simple type of a tropical line and for this type we show that it can have at most $\sum_{i=1}^{n-2}i$ selfintersection points.
Reduction in natural speech
(2009)
Natural (conversational) speech, compared to cannonical speech, is earmarked by the tremendous amount of variation that often leads to a massive change in pronunciation. Despite many attempts to explain and theorize the variability in conversational speech, its unique characteristics have not played a significant role in linguistic modeling. One of the reasons for variation in natural speech lies in a tendency of speakers to reduce speech, which may drastically alter the phonetic shape of words. Despite the massive loss of information due to reduction, listeners are often able to understand conversational speech even in the presence of background noise. This dissertation investigates two reduction processes, namely regressive place assimilation across word boundaries, and massive reduction and provides novel data from the analyses of speech corpora combined with experimental results from perception studies to reach a better understanding of how humans handle natural speech. The successes and failures of two models dealing with data from natural speech are presented: The FUL-model (Featurally Underspecified Lexicon, Lahiri & Reetz, 2002), and X-MOD (an episodic model, Johnson, 1997). Based on different assumptions, both models make different predictions for the two types of reduction processes under investigation. This dissertation explores the nature and dynamics of these processes in speech production and discusses its consequences for speech perception. More specifically, data from analyses of running speech are presented investigating the amount of reduction that occurs in naturally spoken German. Concerning production, the corpus analysis of regressive place assimilation reveals that it is not an obligatory process. At the same time, there emerges a clear asymmetry: With only very few exceptions, only [coronal] segments undergo assimilation, [labial] and [dorsal] segments usually do not. Furthermore, there seem to be cases of complete neutralization where the underlying Place of Articulation feature has undergone complete assimilation to the Place of Articulation feature of the upcoming segment. Phonetic analyses further underpin these findings. Concerning deletions and massive reductions, the results clearly indicate that phonological rules in the classical generative tradition are not able to explain the reduction patterns attested in conversational speech. Overall, the analyses of deletion and massive reduction in natural speech did not exhibit clear-cut patterns. For a more in-depth examination of reduction factors, the case of final /t/ deletion is examined by means of a new corpus constructed for this purpose. The analysis of this corpus indicates that although phonological context plays an important role on the deletion of segments (i.e. /t/), this arises in the form of tendencies, not absolute conditions. This is true for other deletion processes, too. Concerning speech perception, a crucial part for both models under investigation (X-MOD and FUL) is how listeners handle reduced speech. Five experiments investigate the way reduced speech is perceived by human listeners. Results from two experiments show that regressive place assimilations can be treated as instances of complete neutralizations by German listeners. Concerning massively reduced words, the outcome of transcription and priming experiments suggest that such words are not acceptable candidates of the intended lexical items for listeners in the absence of their proper phrasal context. Overall, the abstractionist FUL-model is found to be superior in explaining the data. While at first sight, X-MOD deals with the production data more readily, FUL provides a better fit for the perception results. Another important finding concerns the role of phonology and phonetics in general. The results presented in this dissertation make a strong case for models, such as FUL, where phonology and phonetics operate at different levels of the mental lexicon, rather than being integrated into one. The findings suggest that phonetic variation is not part of the representation in the mental lexicon.
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.
Specific functions of biological systems often require conformational transitions of macromolecules. Thus, being able to describe and predict conformational changes of biological macromolecules is not only important for understanding their impact on biological function, but will also have implications for the modelling of (macro)molecular complex formation and in structure-based drug design approaches. The “conformational selection model” provides the foundation for computational investigations of conformational fluctuations of the unbound protein state. These fluctuations may reveal conformational states adopted by the bound proteins. The aim of this work is to incorporate directional information in a geometry-based approach, in order to sample biologically relevant conformational space extensively. Interestingly, coarse-grained normal mode (CGNM) approaches, e.g., the elastic network model (ENM) and rigid cluster normal mode analysis (RCNMA), have emerged recently and provide directions of intrinsic motions in terms of harmonic modes (also called normal modes). In my previous work and in other studies it has been shown that conformational changes upon ligand binding occur along a few low-energy modes of unbound proteins and can be efficiently calculated by CGNM approaches. In order to explore the validity and the applicability of CGNM approaches, a large-scale comparison of essential dynamics (ED) modes from molecular dynamics (MD) simulations and normal modes from CGNM was performed over a dataset of 335 proteins. Despite high coarse-graining, low frequency normal modes from CGNM correlate very well with ED modes in terms of directions of motions (average maximal overlap is 0.65) and relative amplitudes of motions (average maximal overlap is 0.73). In order to exploit the potential of CGNM approaches, I have developed a three-step approach for efficient exploration of intrinsic motions of proteins. The first two steps are based on recent developments in rigidity and elastic network theory. Initially, static properties of the protein are determined by decomposing the protein into rigid clusters using the graph-theoretical approach FIRST at an all-atom representation of the protein. In a second step, dynamic properties of the molecule are revealed by the rotations-translations of blocks approach (RTB) using an elastic network model representation of the coarse-grained protein. In the final step, the recently introduced idea of constrained geometric simulations of diffusive motions in proteins is extended for efficient sampling of conformational space. Here, the low-energy (frequency) normal modes provided by the RCNMA approach are used to guide the backbone motions. The NMSim approach was validated on hen egg white lysozyme by comparing it to previously mentioned simulation methods in terms of residue fluctuations, conformational space explorations, essential dynamics, sampling of side-chain rotamers, and structural quality. Residue fluctuations in NMSim generated ensemble is found to be in good agreement with MD fluctuations with a correlation coefficient of around 0.79. A comparison of different geometry-based simulation approaches shows that FRODA is restricted in sampling the backbone conformational space. CONCOORD is restricted in sampling the side-chain conformational space. NMSim sufficiently samples both the backbone and the side-chain conformations taking experimental structures and conformations from the state of the art MD simulation as reference. The NMSim approach is also applied to a dataset of proteins where conformational changes have been observed experimentally, either in domain or functionally important loop regions. The NMSim simulations starting from the unbound structures are able to reach conformations similar to ligand bound conformations (RMSD < 2.4 Å) in 4 out of 5 cases of domain moving proteins. In these four cases, good correlation coefficients (R > 0.7) between the RMS fluctuations derived from NMSim generated structures and two experimental structures are observed. Furthermore, intrinsic fluctuations in NMSim simulation correlate with the region of loop conformational changes observed upon ligand binding in 2 out of 3 cases. The NMSim generated pathway of conformational change from the unbound structure to the ligand bound structure of adenylate kinase is validated by a comparison to experimental structures reflecting different states of the pathway as proposed by previous studies. Interestingly, the generated pathway confirms that the LID domain closure precedes the closing of the NMPbind domain, even if no target conformation is provided in NMSim. Hence, the results in this study show that, incorporating directional information in the geometry-based approach NMSim improves the sampling of biologically relevant conformational space and provides a computationally efficient alternative to state of the art MD simulations.
This thesis describes the structural characterization of interactions between biological relevant ribonucleic acid biomacromolecules (RNAs) and selected ligands to optimize the methodologies for the design of pharmacological lead compounds. To achieve this aim, not only the structures of the RNA, the ligand and their complexes need to be known, but also information about the inherent dynamics, especially of the target RNA, are necessary. To determine the structure and dynamics of these molecules and their complexes, liquid state nuclear magnetic resonance spectroscopy (NMR) is a suitable and powerful method. The necessity for these investigations arises from the lack of knowledge in RNA-ligand interactions, e.g. for the development of new medicinal drugs targeting crucial RNA sequences. In the first chapters of this thesis (Chapters II to IV), an introduction into RNA research is given with a focus on RNA structural features (Chapter II), into the interacting molecules, the biology of the specific RNA targets and the further development of their ligands (Chapter III) and into the NMR theory and methodologies used within this thesis (Chapter IV). Chapter II begins with a description of RNA characteristics and functions, placing the focus on the increasing attention that these biomacromolecules have attracted in recent years due to their diverse biological functionalities. This is followed by a detailed description of general structural features of RNA molecules. The biological functions of the RNAs investigated in this thesis (Human immunodeficiency virus PSI- and TAR-RNA and Coxsackievirus B3 Stemloop D in the 5’-cloverleaf element), together with their known structural characteristics are introduced in Chapter III. Furthermore, a description of the investigated ligands is given, focusing on the methods how their affinity and specificity were determined. The introduction is completed in Chapter IV, where the relevant NMR theory and methodologies are explained. First, kinetics and thermodynamics of ligand binding are summarized from an NMR point of view. Subsequently, a detailed description of the resonance assignment procedures for RNAs and peptidic ligands is given. This procedure mainly concentrates on the assignment of the proton resonances, which are essential for the later structure calculation from NMR restraints. The procedure for NMR structure calculation of RNA and its complexes follows with a short introduction into the programs ARIA and HADDOCK. The final part of this chapter explains the relaxation theory and the methodology to extract dynamic information from autocorrelated relaxation rates via the model-free formalism. In the Chapters V to VII of this thesis, the original publications are included and grouped into three topics. Chapter V comprehends the publications on the investigations of HIV PSI-RNA and its hexapeptidic ligand. These three publications[1-3] focus on the characterization of the ligand and its binding properties, its structure and the optimization of its composition aiming to improve its usage for further spectroscopic investigations.
The aim of the study was to investigate the role of the CX3C chemokine FKN in the role of platelet adhesion. The presence of the FKN receptor CX3CR1 in platelets is demonstrated and G-protein dependent activation of platelets with soluble FKN results in the increased adhesion of platelets to collagen and fibrinogen under flow 228 and adhesion of leucocytes to firmly attached platelets 231. Whether membrane-bound FKN is capable to promote the direct adhesion of platelets in flowing blood analogue to leucocytes was completely unknown. The adhesion mechanisms of FKN in mediating the adhesion of leucocytes under flow are well characterised and represent a novel unique mechanism of leucocyte capture and firm adhesion: FKN is responsible for immediate arrest of flowing CX3CR1 expressing leucocytes without the participation of additional adhesion receptors and ligands. This is in contrast to the classical leucocyte adhesion pathways, which are multistep processes involving leucocyte arrest, rolling and subsequent cell activation prior to firm arrest. In leucocytes, the FKN – CX3CR1 axis is sufficient to allow rapid arrest of leucocytes at low shear flow conditions 67, 101, 115, 122, 261. The set of data from this study demonstrates that immobilised FKN was capable to mediate the adhesion of platelets under low shear conditions, whereas there was no interaction in the absence of shear flow. In the presence of vWf in the adhesion matrix, FKN mediated the potent increased adhesion of platelets. This was in parts due to the activation of flowing platelets via CX3CR1 and the augmented translocation of platelets on FKN via the vWf receptor GPIbα. With respect to platelet activation, the function of endothelial FKN was comparable to leucocytes: in both cell types, the FKN dependent activation is mediated by its cognate receptor CX3CR1. This is in contrast to the adhesive capacity: in leucocytes, FKN dependent adhesion is mediated by CX3CR1, whereas in platelets, the adhesive capacity was mostly mediated by the vWf receptor GPIbα with only minor contribution from CX3CR1. In platelets, activation and adhesion by FKN were mediated by two distinct receptors, whereas in leucocytes, CX3CR1 is solely responsible for FKN dependent activation and adhesion. The presented results point out to a role of platelets in early stage of atherosclerosis. The in vivo expression of both, FKN and vWf is regulated by TNF-α, which is released in early stages of inflammation. The presence of vWf and FKN in the endothelial lining of blood vessels during these conditions is sufficient to initiate the capturing and translocation of platelets on the tunica interna. The rolling of platelets on the endothelium can induce endothelial damage and inflammation of the vessel, which might advance to the generation of clinically significant atherosclerotic plaques and fibrous atheroma.
Höhere Eukaryoten stellen ein Ensemble von Zellen dar, die in Kompartimente unterteilt sind. Somit sind intra- und interzelluläre Transportprozesse entscheidend für das Überleben dieser Zellverbände. In meiner Arbeit habe ich Evolution und Struktur von Translokationskomplexen untersucht, um einige Aspekte dieser komplexen Systeme zu untersuchen. Eingangs befassten wir uns mit Rezeptorsystemen am Beispiel des Proteintransports. Mittels phylogenetischer Analysen fanden wir heraus, dass Pex5 nicht der Urahn der anderen untersuchten 3-TPR-Domänen ist, obwohl Pex5 in allen eukaryotischen Organismen vorkommt. Ein Vergleich der 3-TPR-Domänen mit der restlichen Sequenz des Rezeptorproteins ergab, dass die 3-TPR-Domänen eine langsamere Evolutionsgeschwindigkeit aufweisen, was für eine Evolutionseinschränkung durch Interaktionspartner spricht. Sec72 ist möglicherweise aus einer TPR1 (Hop) Domäne entstanden und eine Funktion als Hsp70-erkennende Komponente des Sec-Komplexes für den post-translationalen Import kann daraus abgeleitet werden. „Recycling“ von 3-TPR-Domänen anderer Proteine konnten wir durch unsere phylogenetische Analyse auch für die zweite 3-TPR-Domäne von Tom34 nachweisen, die mit CYP40/FKBP51/52 clustert. Darüber hinaus war es uns möglich, die plastidär bzw. mitochondriell lokalisierten Formen von Toc64 phylogenetisch zu unterscheiden. Durch Erzeugung von Homologiemodellen konnten organellspezifische Aminosäuren strukturell eingeordnet werden. Dabei stellten wir fest, dass sich fast alle Positionen, die sich in der Aminosäurekomposition unterscheiden, auf der konvexen Seite der 3-TPR-Domäne befinden. Molekulardynamische Simulationen zeigten zudem deutliche Veränderung der Hauptbewegungen der 3-TPR-Domänen nach Komplexierung mit dem Hsp90-C-Terminus. Bei Bindung des Liganden werden intramolekulare Wasserstoffbrücken sowohl auf der konvexen als auch konkaven Seite der 3-TPR-Domäne „umgeschaltet“. Diese Erkenntnisse führen zu zwei Hypothesen: 1.) die Organellspezifität der Rezeptoren wird durch die Interaktion mit anderen Komplexpartnern garantiert und 2.) die Änderungen des Wasserstoffbrückennetzwerkes auf der konvexen Seite nach Hsp90-Bindung führen zur Ausbildung der Bindungsstelle für die andere Komplexkomponente. Beide Hypothesen erklären die experimentellen Beobachtungen bezüglich der Rezeptoren und warum keine phylogenetischen Hinweise für die Existenz von Vorstufenprotein-spezifischen Hsp70/90-Proteinen gefunden werden konnten. Nach dem Rezeptor haben wir uns mit dem Translokationsprozess befasst. Wir konnten phylogenetisch zeigen, dass sich Omp85 aus Proteobakterien im Vergleich zu Cyanobakterien und Eukaryoten insbesondere durch andersartige POTRA Domänen auszeichnet und fanden zwei konservierte Motive in der Porenregion. Zudem konnten wir im Heterokontophyten P. tricornutum ein vollständiges Omp85 identifizieren (bipartite Signalsequenz, 2 POTRAs, Pore mit langen Schleifen). Die Aminosäuresequenz weicht teils deutlich von den bekannten Omp85-Proteinen ab, was die Entdeckung erschwerte. Wir haben damit geklärt, dass auch im Translokationsapparat von komplexen Plastiden ein b-Fassprotein der Omp85 Familie die Kerneinheit bildet. Ebenfalls zu den Protein-transportierenden b-Fassproteinen gehört TolC, das aber im Gegensatz zu Omp85 auch andere Substanzen, wie zum Beispiel Siderophore transportiert. Alr2887 ist das einzige TolC-ähnliche Protein aus Anabaena sp. PCC7120. Vergleichende Phänotypuntersuchungen weisen auf eine Interaktion eines ABC-Transporters (DevBCA Operon) mit Alr2887 hin. Die Distanz zwischen äußerer Membran und Plasmamembran ist in Anabaena doppelt so groß wie in E. coli. Entsprechend fanden wir im Adapterprotein DevB eine stark verlängerte dimere Doppelwendel, die das von TolC gebildete a-Fass im Periplasma bis hin zum ABC-Transporter in der Plasmamembran theoretisch fortsetzen kann. Da verschiedenste in Anabaena existierende ABC-Transporter TolC als Abflusskanal benötigen, nehmen wir an, dass Alr2887 ein Rundumtalent in Bezug auf die zu transportierenden Substrate darstellt. Dieses ist auch aufgrund der basalen Einordnung im phylogenetischen Baum zu vermuten; es könnte somit auch in den „Multi-Drug-Efflux“ involviert sein. Nicht nur ABC-Transporter, auch TonB-abhängige Transporter stehen in funktionellem Zusammenhang mit TolC. Wir haben Aminosäuresequenzen von ~4600 TBDTs aus Gram-negativen Bakterien und Cyanobakterien zusammengetragen und nach ihrer paarweisen Ähnlichkeit geclustert. Anhand experimentell charakterisierter TBDTs mit bekannten Substraten und TBDTs mit vorhergesagten Substraten konnten wir sehr vielen Clustern ein Substrat zuordnen, das die in ihnen zusammengefassten TBDTs aller Wahrscheinlichkeit nach importieren. Wir konnten ferner feststellen, dass es noch eine Menge weiterer Cluster mit unbekannten Substratspezifitäten gibt und unsere Analysen stimulieren somit die Arbeiten an diesem System im Allgemeinen und in Cyanobakterien im Besonderen.
Die anaerobe Atmung mit Nitrat und Nitrit als terminalen Elektronenakzeptoren bildet einen wichtigen Teil des biologischen Stickstoff-Zyklus. Beispiele sind Denitrifikation und respiratorische Nitrat-Ammonifikation, wobei in beiden Fällen in einem ersten Schritt Nitrat zu Nitrit reduziert wird. In der Denitrifikation entstehen dann verschiedene gasförmige Produkte (NO, N2O, N2), wogegen Nitrit in der Ammonifikation ohne die Freisetzung weiterer Zwischenprodukte direkt zu Ammonium reduziert wird. Während die terminalen Reduktasen dieser Atmungsketten gut untersucht sind, ist das Wissen über die Zusammensetzung kompletter Elektronentransportketten sowie die Interaktion einzelner Proteine als auch zwischen den Proteinen und Chinonen in der Membran begrenzt. Ziel dieser Arbeit war die Charakterisierung der membranständigen Chinol-Dehydrogenasen NapGH und NrfH in der respiratorischen Nitrat-Ammonifikation von Wolinella succinogenes. Dieses Epsilonproteobakterium ist ein etablierter Modellorganismus der anaeroben Atmung und wächst durch respiratorische Nitrat-Ammonifikation mit Formiat oder H2 als Elektronendonoren. Als terminale Reduktasen werden dabei die periplasmatische Nitratreduktase NapA und die Cytochom c-Nitritreduktase NrfA benötigt. Die Genomsequenz weist keine weiteren typischen Nitrat- und Nitritreduktasen auf, und napA- und nrfA-defiziente Mutanten sind nicht in der Lage durch Nitrat- bzw. Nitritatmung wachsen. Das Operon des Nap-Systems (napAGHBFLD) von W. succinogenes kodiert Proteine, die an der Nitrat-Reduktion durch Menachinol beteiligt sind (NapA, -B, -G und -H) und Proteine, die für die Reifung und Prozessierung von NapA benötigt werden (NapF, -L und –D). Im Gegensatz zu vielen anderen Bakterien läuft die Nitrat-Atmung unabhängig von einem NapC-ähnlichen Protein ab, das als membrangebundenes Tetrahäm-Cytochrom c für die Chinol-Oxidation zuständig ist und Elektronen über den Elektronenüberträger NapB an die terminale Reduktase NapA liefert. Zwar sind im Genom zwei NapC-Homologe kodiert (FccC und NrfH), doch die Deletion beider Gene hatte keinen Einfluss auf die Nitrat-Atmung. Es wurde vermutet, dass die Funktion von NapC in W. succinogenes stattdessen durch die beiden Fe/S-Cluster Proteine NapG und NapH übernommen wird. Die Reduktion von Nitrit zu Ammonium wird durch den NrfHA-Komplex katalysiert. Das Pentahäm-Cytochrom c NrfA bildet dabei die katalytische Untereinheit, die über das membranständige Tetrahäm-Cytochrom c auf der periplasmatischen Seite der Membran gebunden ist. NrfH gehört zur NapC/NirT-Familie und überträgt Elektronen von Menachinol auf NrfA. Mittels gerichteter Mutagenese von nrfH wurden in früheren Arbeiten bereits Aminosäure-Reste identifiziert, die essentiell für die Elektronentransportaktivität von Formiat zu Nitrit sind.