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In April and May 2012 data on Au+Au collisions at beam energies of Ekin = 1.23A GeV were recorded with the High Acceptance Di-Electron Spectrometer, which is located at the GSI Helmholtz Center for Heavy Ion Research in Darmstadt, Germany. At this beam energy all hadrons containing strangeness are produced below their elementary production threshold. The required energy is not available in binary NN collisions but must be provided by the system e.g. through multi-particle interactions or medium effects like a modified in-medium potential (e.g. KN/ΛN potential). Thus, a high sensitivity to these medium effects is expected in the investigated system.
The baryon-dominated systems created in relativistic heavy-ion collisions (HIC) at SIS18 energies reach densities of about 2-3 times ground state density p0 and may be similar to the properties of matter expected in the inner core of neutron stars. It is in particular the behavior of hadrons containing strangeness, i.e. kaons and hyperons, and their potentials in the dense medium which may have severe implications on astrophysical objects and processes. As ab-initio calculations of quantum chromodynamics (QCD) cannot be performed rigorously on the lattice at finite baryo-chemical potentials due to the fermion sign problem, effective descriptions have to be used in order to model properties of dense systems and the involved particles. The only way to access the in-medium potential of strange hadrons above nuclear ground state density p0 is by comparing data from relativistic HIC to such effective microscopic models. Up to now, not much data on neutral kaons and Λ hyperons are available from heavy collision systems close to their NN production threshold. These two electromagnetically uncharged strange hadrons are in particular well suited to study their potential in a dense nucleon-dominated environment as their kinematic spectra are not affected by Coulomb interactions.
Alzheimer’s Disease (AD) is the most common neurodegenerative disorder marked by progressive loss of memory and cognitive ability. The pathology of AD is characterised by the presence of amyloid plaques, intracellular neurofibrillary tangles and pronounced cell death. The aim of this thesis was to investigate pathways involved in the Aß cascade of neurodegeneration. Since novel findings indicate that already this Aß species exerts neurotoxic effects long before hyperphosphorylated tau, neurofibrillary tangles and extracellular Aß plaques appear, the investigations were accomplished with specific regard to the effects of intracellular Aß. The Swedish double mutation in the APP gene results in six- to eightfold increased Aß production of both Aß1-40 and Aß1-42 compared to human wildtype APP cells (APPwt). Data obtained from PC12 cells indicate that it is possible to specifically increase the Aß load without enhancing APP expression levels. On the basis of these findings, it seemed possible to investigate dose-dependent effects of Aß in multiple experimental designs. These assay designs were created in order to mimick different in-vivo situations that are discussed to occur in AD patients: APPsw PC12 cells exhibit low physiological concentrations of Aß within picomolar range in contrast to APPsw HEK cells, expressing Aß levels within the nanomolar range. Of note, the APPsw HEK cells showed a specific and highly significant increase in the intracellular accumulation of insoluble Aß1-42. Moreover, an intracellular accumulation of Aß and APP was found in the mitochondria of the HEK APPsw cells suggesting a direct impact on mitochondrial function on these cells. This effect might finally lead to disturbances in the energy metabolism of the cell or to increased cell death. Furthermore, baseline g- and ß-secretase activity was assessed since these enzymes represent promising therapeutic targets to slow or halt the disease process. As expected, ß-secretase activity was significantly elevated in all APPsw cell lines. This might be due to the proximity of the Swedish double mutation next to the N-terminus of the Aß sequence. Interestingly, g-secretase activity was similarly increased in PC12 APPsw cells. In addition, the toxicity of different Aß species was investigated in SY5Y and PC12 cells with regard to their effect on cellular viability mirrored by mitochondrial activity using MTT assay. Here, it turned out that not monomers, but already dimers are neurotoxic correlates. Fibrillar Aß species showed the highest toxicity. In the next step, SY5Y cells forming endogenous, dimeric APP and Aß were investigated. In accordance with previous findings, these cells showed a decreased MTT reduction potential in comparison to APPwt and control SY5Y cells reflecting a decrease of cellular viability. The impaired energy metabolism of the cells was even more drastically mirrored by reduced baseline ATP levels. In the second part of this thesis, the expression and intracellular distribution of Bcl-2 family proteins and pro-apoptotic mitochondrial factors under baseline conditions and during oxidative stress were analyzed in the APPwt and APPsw bearing cells. The most prominent finding was the reduction of expression levels of the anti-apoptotic factor Bcl-xL in the cytosolic fractions of APPwt and APPsw PC12 cells. This might indicate that a lack of anti-apoptotic factors or their altered intracellular distribution, rather than an increase in caspase-dependent pro-apoptotic factors, could be responsible for the increased vulnerability of APPwt- and APPsw-transfected PC12 cells against oxidative stress. Since total Bcl-xL expression was unaffected in PC12 cells, in contrast to APPwt and APPsw-expressing SY5Y and HEK cells revealing significantly decreased Bcl-xL expression levels. Thus, alterations in Bcl-xL distribution seem to be an early event in the disease process. Increasing Bcl-xL expression might potentially be one promising strategy for AD modification. PC12 and HEK cells bearing APPsw or APPwt were treated with the potent g-secretase inhibitor DAPT. Of note, DAPT did not only efficiently block Aß production, but additionally led to an elevation of the MTT reduction potential, reflecting an increase in cellular viability. As another disease-modifying strategy, several efforts are undertaken to ameliorate AD-relevant symptoms by the treatment with nerve growth factor (NGF). Generally, it is known that substituted pyrimidines have modest growth-promoting effects. Here, KP544, a novel substituted pyrimidine, was characterised. This drug increased MTT reduction potential in terminally differentiated and undifferentiated PC12 cells. Furthermore, treatment with KP544 led to a reduction in Aß1-40 secretion. Thus, one may conclude that the target of KP544, GSK-3ß, represents a connecting link between the two main pathological hallmarks of AD and might thus be a very promising therapeutic target for AD.
Glioblastoma is the most common and most aggressive type of brain tumor in adults. In contrast to epithelial cancers, glioblastomas do not metastasize. While the major treatment challenge in epithelial cancers is not the primary tumor but metastasis, glioblastoma patients die of the primary tumor.
However, there is a common theme which underlies the malignant properties of progressed epithelial cancers and glioblastoma: invasion from the primary tumor into the surrounding tissue. In the case of epithelial cancers this is the first and necessary step to metastasis, whereas invasion leads inevitably to tumor recurrence after resection in the case of glioblastoma, causing it to be incurable.
A cellular program which has been described in detail to promote the invasive phenotype in epithelial tumors, is the epithelial-mesenchymal-transition (EMT). Differentiated neural cells are not epithelial, thus, strictly speaking, EMT does not occur in glioblastoma. However, the traits acquired in the process of EMT, especially invasiveness and stemness, are highly relevant to glioblastoma. One of the key transcription factors known to induce EMT in epithelial cancers is ZEB1, which has been described only marginally in the central nervous system so far. Here, I investigate the expression and function of ZEB1 in glioblastoma and during human fetal neural development.
ZEB1 mRNA was significantly upregulated in all histological types of glioma, including glioblastoma, when compared to normal brain. There was no correlation between ZEB1 mRNA levels and tumor grade. Immunohistochemical staining of glioma samples demonstrated that ZEB1 was highly expressed in the great majority of tumor cells. In the developing human brain, intense staining for ZEB1 could be observed in the ventricular and subventricular zone, where stem- and progenitor cells reside. ZEB1 positive cells included cells stained with stem- and progenitor markers like PAX6, GFAP and Nestin. In contrast, ZEB1 was never found in early neuronal cells as identified by TUBB3 staining.
To gain insight into ZEB1 function I generated a human fetal neural stem cell line and a glioblastoma cell line with ZEB1 knockdown, which were compared with their respective control cell lines. First, I found that ZEB1 does not regulate the micro RNA 200 family in either cell line, which has been described as an essential ZEB1 target in epithelial cancers. Second, regulated target genes were identified with a genome wide microarray. The third approach was to directly identify genomic binding sites of ZEB1 by chromatin immunoprecipitation sequencing (ChIP-seq). All three approaches showed that the ZEB1 transcriptional program is surprisingly similar in the neural stem cell line and the glioblastoma cell line. In contrast, it bears only little resemblance to the program described in epithelial cancers.
The most interesting, previously unrecognized ZEB1 target gene identified in this study is integrin b1. It was regulated after ZEB1 knockdown detected by microarray analysis, and has a ZEB1 binding site in its promoter region detected by ChIP-seq. Finally, I addressed the question whether ZEB1 influences tumor growth and invasiveness in a glioblastoma model. After intracranial xenotransplantation in mice, ZEB1 knockdown glioblastoma cells formed significantly smaller and less invasive tumors than control glioblastoma cells.
This study demonstrates that ZEB1 is widely expressed in glioma and relevant for glioblastoma growth and invasion. In contrast to what is known about ZEB1 function in epithelial cancers, ZEB1 is not associated with glioma progression, but instead seems to be an early and necessary event in tumorigenesis. Also with regard to ZEB1 target genes, ZEB1 functions differently in glioblastoma than in epithelial cancers. The two most important ZEB1 targets in epithelial cancers are E-cadherin and the miR-200 family members. Both are not relevant to ZEB1 function in glioblastoma. Interestingly, while the ZEB1 transcriptional program is different from the one described in epithelial cancers, it is highly similar in glioblastoma cells and fetal neural stem cells. This suggests that an embryonic pathway restricted to stem- and progenitor cells during development is reactivated in glioblastoma.
Previously known ZEB1 target genes were tissue specific and therefore seemed unlikely to mediate ZEB1 function in the central nervous system. However, the newly identified ZEB1 target gene integrin b1 is well known to play pivotal roles in both glioblastoma tumorigenesis and invasion as well as in neural stem cells. Additionally, integrin b1 is widely expressed and seems a likely ZEB1 target in other organs than the brain.
Taken together, I demonstrate that ZEB1 is a new regulator of glioblastoma growth and invasion. The transcriptional program of ZEB1 differs from the one in epithelial cancers but is strikingly similar to the one in neural stem cells. The newly identified ZEB1 target gene integrin b1 is likely to mediate crucial ZEB1 functios. Thus, this study identifies ZEB1 as a yet unrecognized player in glioblastoma and neural development. Furthermore, it sets the stage for more research which will help to deepen our understanding of ZEB1 function in the central nervous system and beyond.
Human GLUTs represent a family of specialized transporters that facilitate the diffusion of hexoses through membranes along a concentration gradient. The 14 isoforms share high sequence identity but differ in substrate specificity and affinity, and tissue distribution. According to their structure similarity, GLUTs are divided into three classes, with class 1 comprising the most intensively studied isoforms GLUTs1 4. An abnormal function of different GLUT members has been related to the pathogenesis of various diseases, including cancer and diabetes. Hence, GLUTs are the subject of intensive research, and efforts concentrate on identifying GLUT-selective ligands for putative medical purposes and their application in studies aiming to further unravel the metabolic roles of these transporters.
The hexose transporter deficient (hxt0) yeast strain EBY.VW4000 is devoid of all its endogenous hexose transporters and unable to grow on glucose or related hexoses. This strain has proven to be a valuable platform to investigate heterologous transporters due to its easy handling, increased robustness, and versatile applications. However, the functional expression of GLUTs in yeast requires certain modifications. Single point mutations of GLUT1 and GLUT5 led to their functional expression in EBY.VW4000, whereas the native GLUT1 was actively expressed in EBY.S7, a hxt0 strain carrying the fgy1 mutation that putatively reduces the phosphatidylinositol-4-phosphate (PI4P) content in the plasma membrane. GLUT4 was only actively expressed in the hxt0 strain SDY.022, which also contains the fgy1 mutation and in which ERG4 is additionally deleted. Erg4 is one of the late enzymes in the ergosterol pathway, and therefore SDY.022 probably has an altered sterol composition in its membrane.
The goal of this thesis was to actively express GLUT2 and GLUT3 in a hxt0 yeast strain, providing a convenient system for their ligand screening. A PCR-derived amino acid exchange in the sequence of GLUT3 enabled its functional expression in EBY.VW4000 and the unmodified GLUT3 protein was active in EBY.S7. Functional expression of GLUT2 was achieved by rational design. The extracellular loop between the transmembrane regions 1 and 2 is significantly larger in GLUT2 than in other class 1 GLUTs. By truncating this loop by 34 amino acids and exchanging an alanine for a serine, a GLUT3-like loop was implemented. The resulting construct GLUT2∆loopS was functional in EBY.S7. With an additional point mutation in the transmembrane region 11, GLUT2∆loopS_Q455R was also actively expressed in EBY.VW4000. Inhibition studies with the known GLUT inhibitors phloretin and quercetin showed a reduced transporter activity for GLUT2 and GLUT3 in uptake assays and growth tests when inhibitors were present, demonstrating that both systems are amenable for ligand screening experiments.
The newly established GLUT2 yeast system was then used to screen a library of compounds pre-selected by in silico screening. Thereby, eleven identified GLUT2 inhibitors exhibited strong potencies with IC50 values ranging from 0.61 to 19.3 µM. By employing the other yeast systems, these compounds were tested for their effects on GLUT1, and GLUTs3-5, revealing that nine of the identified ligands were GLUT2-selective. In contrast, one was a pan-class 1 inhibitor (inhibiting GLUTs1-4), and one affected GLUT2 and GLUT5, the two fructose transporting isoforms. These compounds will serve as useful tools for investigations on the role of GLUT2 in metabolic diseases and might even evolve into pharmaceutical agents targeting GLUT2-associated diseases.
Due to the beneficial effect of the putatively changed sterol composition in SDY.022 (by ERG4 deletion) on the functional expression of GLUT4, it was hypothesized that the presence of the human sterol cholesterol, or cholesterol-like sterols, might have a beneficial effect on GLUT expression, too. Thus, it was attempted to generate hxt0 strains that synthesize these sterols by genetic modifications targeting the ergosterol pathway. In the scope of these experiments, several strains with different sterol compositions were generated. Drop tests on glucose medium with the different strains expressing GLUT1 or GLUT4 revealed that the deletion of ERG6 is clearly advantageous for a functional expression of GLUT1 (but not GLUT4). This indicates that the methyl group at the ergosterol side chain (introduced by Erg6 and reduced by Erg4) negatively influences GLUT1 activity. However, this effect on GLUT1 activity was less pronounced than the putative altered PI4P content in EBY.S7.
Additionally, in this thesis, a new tool to measure glucose transport rates of transporters expressed in the hxt0 yeast system was developed to facilitate their kinetic characterization. For this, the pH-sensitive GFP variant pHluorin was employed as a biosensor for the cytosolic pH (pHcyt) by measuring the ratio (R390/470) of emission intensities at 512 nm from two different excitation wavelengths (390 and 470 nm). Sugar-starved cells exhibit a slightly acidic pHcyt because ATP production is depleted, reducing the activity of ATP-dependent proton pumps.
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The present study was elaborated within the scope of the INTAFERE (Integrated Analysis of Mobile Organic Foreign Substances in Rivers) project which investigates the occurrence of xenobiotics in small freshwater streams with particular consideration of social impact factors. The aim of this study is to investigate the seasonal and spatial variance of organic micropollutants in small fresh water streams and to identify possible sources and sinks. Therefore four small freshwater river systems in Hesse, Germany, have been investigated with respect to common organic pollutants such as: the organophosphates tri-n-butyl phosphate (TBP), tris(2-butoxyethyl)phosphate (TBEP), tris(2-chloroethyl)phosphate (TCEP), tris(1-chloro-2-propyl)phosphate (TCPP), and tris(1,3-dichloro-2-propyl)phosphate (TDCPP), the synthetic musk fragrances 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexa-methylcyclopenta-[g]-2-benzopyran (HHCB) and 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene (AHTN), the endocrine disruptors bisphenol A (BPA), 4-tert-octylphenol (OP) and the technical isomer mixture of 4-nonylphenol (NP), the herbicide terbutryn [2-(t-butylamino)-4-(ethylamino)-6-(methylthio)-s-triazine] as well as the insect repellent N,N-diethyl-m-toluamide (DEET). Water samples were collected in the time span from September 2003 to September 2006 at 26 sampling locations. The samples were extracted with solid phase extraction (SPE) and analyzed by coupled gas chromatography-mass spectrometry (GC-MS). For quantification the internal standard method was used. The results of the study showed an ubiquitous occurrence of organic pollutants in the fresh water streams of the study area. The organophosphates have been detected in 90 % of the water samples with mean concentrations of 502 ng/l (TCPP), 276 ng/l (TBP), 183 ng/l (TBEP), 118 ng/l (TCEP) and 117 ng/l (TDCPP). Sewage treatment plant (STP) effluents were identified as the dominating source for the chlorinated organophosphates as well as for the synthetic musk fragrances and the insect repellent DEET in the river systems. Consequently the highest concentrations were observed in the Schwarzbach system characterized by the highest proportion of waste water compared to the other river systems. Mean concentration levels of the synthetic musk fragrances HHCB and ATHN were 141 ng/l and 46 ng/l, respectively and 124 ng/l in case of DEET. The synthetic musk fragrances showed a clear seasonal trend with significantly lower concentrations in summer times compared to winter times, which is ascribed to stronger photodegradation and volatization during summer times. In contrast, mean DEET concentrations and loads were significantly higher in summer than in autumn, winter and spring, in parallel with the main insect season. The concentrations of the endocrine disruptors BPA, NP and OP in the river water samples ranged from <20 ng/l to 1927 ng/l, <10 ng/l to 770 ng/l, and <10 ng/l to 420 ng/l, respectively. Whereas OP was present in about 2/3 of the samples, NP and BPA could only be detected in 56% and 13% of the water samples, respectively. BPA levels exceeded in two samples the predicted no-effect concentration (PNEC) for water organisms. In case of NP, highest concentrations and loads were found in September 2003 and decreased significantly since then. In contrast, concentrations and loads of OP which serves in a similar application field remained nearly constant during the sampling period. The decrease of NP can be attributed to the implementation of the European Directive 2003/53/EG, which restricts the use of nonylphenols and nonylphenol ethoxylates since January 2005. However, at the end of the sampling period in September 2006, NP could still be detected at mean concentrations of 18 ng/l in the river waters of the sampling area. Furthermore, absence of NP in several samples from associated STP effluents indicate that the STPs cannot be the only sources for NP found in the river water. The herbicide terbutryn was present in the rivers during the whole sampling period from September 2003 to September 2006 despite a ban on its use as a herbicide from January 2004 on. Terbutryn levels ranged from < 4 ng/l to 5600 ng/l, showing a clear spatial pattern with high terbutryn concentrations in the Weschnitz and Modau river systems and significantly lower terbutryn levels in Schwarzbach and Winkelbach. Results from the analysis of two STP effluents discharging into the Weschnitz and the Modau, respectively, indicate that terbutryn enters the rivers from this source. Furthermore, terbutryn concentrations and loads showed a clear seasonal trend with significantly higher levels in summer and autumn. Obviously, the ban on agricultural use of terbutryn at the end of 2003 had no discernable influence on terbutryn concentration in the rivers because there was no trend of decreasing.
X-ray structure of the Na+-coupled Glycine-Betaine symporter BetP from Corynebacterium glutamicum
(2009)
Cellular membranes are important sites of interaction between cells and their environment. Among the multitude of macromolecular complexes embedded in these membranes, transporters play a particularly important role. These integral membrane proteins perform a number of vital functions that enable cell adaptation to changing environmental conditions. Osmotic stress is a major external stimulus for cells. Bacteria are frequently exposed to either hyperosmotic or hypoosmotic stress. Typical conditions for soil bacteria, such as Corynebacterium glutamicum, vary between dryness and sudden rainfall. Physical stimuli caused by osmotic stress have to be sensed and used to activate appropriate response mechanisms. Hypoosmotic stress causes immediate and uncontrolled influx of water. Cells counteract by instantly opening mechanosensitive channels, which act as emergency valves leading to fast efflux of small solutes out of the cell, therebydiminishing the osmotic gradient across the cell membrane. Hyperosmotic stress, on the other hand, results in water efflux. This is counterbalanced by an accumulation of small, osmotically active solutes in the cytoplasm, the so-called compatible solutes. They comprise a large variety of substances, including amino acids (proline), amino acid derivatives (betaine, ectoine), oligosaccharides (trehalose), and heterosides (glucosylglycerol). Osmoregulated transporters sense intracellular osmotic pressure and respond to hyperosmotic stress by facilitating the inward translocation of compatible solutes across the cell membrane, to restore normal hydration levels. This work presents the first X-ray structure of a member of the Betaine-Choline-Carnitine-Transporter (BCCT) family, BetP. This Na+-coupled symporter from Corynebacterium glutamicum is a highly effective osmoregulated and specific uptake system for glycine-betaine. X-ray structure determination was achieved using single wavelength anomalous dispersion (SAD) of selenium atoms. Selenium was incorporated into the protein during its expression in methione auxotrophic E. coli cells, grown in media supplemented with selenomethionine. SAD data with anomalous signal up to 5 Å led to the detection of 39 selenium sites, which were used to calculate the initial electron density map of the protein. Medium resolution and high data anisotropy made the structure determination of BetP a challenging task. A specific strategy for data anisotropy correction and a combination of various crystallographic programs were necessary to obtain an interpretable electron density map suitable for model building. The crystal structure of BetP shows a trimer with glycine-betaine bound in a three-fold cation-pi interaction built by conserved tryptophan residues. The bound substrate is occluded from both sides of the membrane and aromatic side chains line its transport pathway. Very interestingly, the structure reveals that the alpha-helical C-terminal domain, for which a chemo- and osmosensory function was elucidated by biochemical methods, interacts with cytoplasmic loops of an adjacent monomer. These unexpected monomer-monomer interactions are thought to be crucial for the activation mechanism of BetP, and a new atomic model combing biochemical results with the crystal structure is proposed. BetP is shown to have the same overall fold as three unrelated Na+-coupled symporters. While these were crystallised in either the outward- or inward-facing conformation, BetP reveals a unique intermediate state, opening new perspectives on the alternating access mechanism of transport.
We study the Wigner function for massive spin-1/2 fermions in electromagnetic fields. The Wigner function is analytically solved in five cases when electromagnetic fields are constants. For a general space-time dependent field configuration, we use the method of semi-classical expansion and solved the Wigner function at linear order in the Planck's constant. At the same order, we obtained a generalized Boltzmann equation for particle distribution, and a generalized BMT equation for spin polarization. Using the Wigner function, we calculated some physical quantities in a thermal equilibrium system.
The substantia nigra is not the induction site in the brain of the neurodegenerative process that underlies Parkinson’s disease. Instead, the results of this semiquantitative study of 30 autopsy cases with incidental Lewy body pathology indicate that Parkinson’s disease in the brain commences with the formation of the very first immunoreactive Lewy neurites and Lewy bodies in noncatecholaminergic visceromotor neurons of the dorsal glossopharyngeusvagus complex, in projection neurons of the intermediate reticular zone, and in specific nerve cell types of the gain setting system (coeruleussubcoeruleus complex, caudal raphe nuclei, gigantocellular reticular nucleus), olfactory bulb, olfactory tract, and/or anterior olfactory nucleus in the absence of nigral involvement. The topographical parcellation of the nuclear grays described here is based upon known architectonic analyses of the human brain stem and takes into consideration the pigmentation properties of a few highly susceptible nerve cell types involved in Parkinson’s disease. In this sample and in all 58 ageand gendermatched controls, Lewy bodies and Lewy neurites do not occur in any of the known telencephalic Parkinson’s disease predilection sites (hippocampal formation, temporal mesocortex, proneocortical cingulate areas, amygdala, basal nucleus of Meynert, interstitial nucleus of the diagonal band of Broca, hypothalamic tuberomamillary nucleus).
Background: Increasing numbers of patients surviving malignant bone tumors around the knee joint have led to an increasing importance to investigate long-term results. This study assessed the long-term results of rotationplasty after resection of malignant bone tumors regarding functional outcome and quality of life to allow better comparison with other treatment options in bone cancer treatment.
Procedure: 60 participants who underwent rotationplasty due to bone cancer took part in this multicentric questionnaire- based study. The long-term functional outcome was measured by the Musculoskeletal tumor society score (MSTS) and the Tegner activity level scale. The health-related quality of life (HRQL) was assessed by using the Short Form Health Survey (SF-36).
Results: Patients treated with rotationplasty (median follow- up of 22 years, range 10–47 years) regained a high level of activity (median MSTS score of 24). Even a return to high level sports was possible (mean Tegner activity level scale of 4). Duration of follow-up did not influence the functional outcome. HRQL scores were comparable to the general German popula tion. Concerns of psychological problems due to the unusual appearance of the rotated foot have not been confirmed.
Conclusion: Rotationplasty can be a good alternative to en- doprosthetic replacement or amputation, either as primary surgery or as a salvage procedure. Especially for growing children and very active patients rotationplasty should be considered.
The cytochrome bc1 complex or ubiquinol:cytochrome c oxidoreductase (QCR) catalyses electron transfer from ubiquinol to cytochrome c in respiration and photosynthesis coupled to a vectorial proton transport across the membrane, in which the enzyme resides. In both bacteria and eukaryotic organisms, QCR participates in supramolecular assembly of membrane proteins that comprise the respiratory or photosynthetic chain. In the present work, proton transfer pathways, substrate binding and the supramolecular assembly of the respiratory chain in yeast were probed by structure-based site-directed mutagenesis and characterization of the variants. Both active sites centre P, the place of quinol oxidation, and centre N, where quinone reduction takes place, lack direct access to the bulk solvent necessary for proton release and uptake. Based on the X-ray structure, proton transfer pathways were postulated. Analysis at centre P showed, that E272 and Y132 of cytochrome b are important for QCR catalysis as indicated by increased superoxide production and lowered Cyc1p reductase activity in these variants. Pre-steady state heme reduction kinetics in combination with stigmatellin resistance indicated that charge and length of the side chain at position 272 are crucial for efficient docking of the ISP to form the enzyme substrate complex and for electron bifurcation at centre P. Variants of Y312 and F129, both residues of cytochrome b, showed an increased Km indicating participation of these residues in coordination of ubiquinol or the possible intermediate semiquinone anion radical. F129 proved to be crucial for a functional Q-cycle as indicated by respiratory negative growth phenotype and a lowered H+/e- stoichiometry of F129 variants. At centre N, the postulated CL/K and E/R proton transfer pathways are located at opposite sites of the bound ubiquinone. Variants in the surface residues R218 (cytochrome b) and E52 (Qcr7) of the E/R pathway and E82 (Qcr7) of the CL/K pathway showed instability upon purification indicating an important role of these residues for QCR integrity. The slowed down centre N reduction kinetics in H85 (CL/K), R218 and N208 (both E/R) variant was attributed to a destabilised semiquinone anion consistent with the observed decreased sensitivity towards the site-specific inhibitor antimycin and an increased Km. Variants of residues of both pathway, E82Q and R218M, exhibited a decreased H+/e- stoichiometry indicating a crucial role of both residue for maintaining a working Q-cycle and supporting the proposed protonation of the substrate via the Cl/K and the E/R pathway. Long-range interaction between centre N and centre P were observed by altered reduction kinetics of the high potential chain and increased superoxide production in the centre N variants. The role of the cation-pi-interaction between F230 of Cyt1p and R19 of cytochrome c in binding of the redox carrier to QCR was analysed. In F230L hydrophobic interaction were partially lost as was deduced from the ionic strength dependence of Cyc1p reductase activity and Cycp1 binding, as detected by ionic strength sensitive Kd and Km for Cyc1p. The decreased enzymatic rate of F230W could be explained by a disturbed binding of Cyc1p to the variant enzyme. F230 may influence the heme mid point potential and thereby the electron transfer rate to Cyc1p. Reduction of Cobp via both centre P and centre N was disturbed suggesting an interaction between high and low potential chain. Supramolecular association between QCR and cytochrome c oxidase (COX) in yeast mitochondria was probed by affinity chromatography of a his-tagged QCR in the presence of the mild detergent digitonin. In comparison to purification with laurylmaltoside, the presence of both QCR and COX subunits was detected in the elution fractions by SDS-PAGE, Cyc1p reductase and TMPD oxidase activity assays and immunoblot analysis. The CL-dependent formation of the supercomplex between QCR and COX was analysed by replacement variants in the CL-binding site of QCR in CL containing and CL free environment. With an increasing number of replacements of the three lysines the CL-binding pocket supercomplex formation was not abolished, when CL is present as shown by BN-PAGE analysis. This was supported by the synergetic decrease in enzyme activity for both enzymes upon increased number of replacements. In the CL-free environment, no supracomplex formation was observed for a wildtype CL binding site. By replacements of two lysines in the CL-binding pocket, supercomplex formation could be recovered as revealed by BN-PAGE. This indicates, that CL may serve as a charge neutralizer for the lysines near the presumed interaction domain between complex III and complex IV. The obtained results for centre P provide new information of residues critical for stabilisation of ubiquinol and controlling electron short circuit reactions. The observations for centre N variants clearly support the proposed two proton transfer pathways and the role of the bound phospholipids in centre N kinetics. Variants in the Cyc1p binding site suggest a role for F230 both in Cyc1p binding and electron transfer. Clear interaction between the high and low potential chain in both Cyt1p and centre N variants strongly support long-range interactions in the complex. Studies on the supramolecular association of complex III and complex IV indicate a new role of Cl in stabilising a supracomplex.
This dissertation contains five independent chapters dealing with wage dispersion and unemployment. The first chapter deals with the explanation of international changes in wage inequality and unemployment in the 80s and 90s. Both theoretically and empirically, social benefits and its link to average income are blamed for the different experiences across countries. The second chapter discusses the search framework, to explain residual wage inequality and finds that institutional wage compression has ambiguous effects on employment. In the third chapter, we apply the theory to German data. We show that job-to-job transitions are important in explaining both frictions and career advances. In the fourth chapter, we empirically assess the relationship between wage dispersion and unemployment for homogeneous workers. We find that neither a frictional nor a neo-classical view in explaining this relationship are convincing. Unemployment within cells is not negatively correlated with wage dispersion. Finally, the last chapter builds a theoretical model which treats heterogeneous individuals in a production function framework and a frictional labor market. The model generates both wage dispersion within and between skill groups and both frictional and structural unemployment. In sum, the dissertation stresses the importance of modelling frictions to understand different types of wage inequality and unemployment.
The dissertation collects four self-contained essays which contribute to the literature on wage structures, heterogeneous labor demand, and the impact of trade unions. The first paper provides a detailed description of the evolution of wage inequality in East and West Germany in the late years of the twentieth century. In contrast to previous decades, wage inequality has been rising in several dimensions during that period. The second paper identifies cohort effects in the evolution of both wages and employment. Observed structures are consistent with a labor demand framework that incorporates steady skill-biased technical change. Substitutability between skill and age groups in the German labor market is found to be relatively high. Simulations based on estimated elasticities of substitution illustrate that higher wage dispersion between skill groups would have contributed to a reduction in unemployment. The third paper estimates determinants of individual union membership decisions and studies the erosion of union density in East and West Germany. Using corresponding predictions of net union density, the fourth paper analyzes the link between union strength and the structure of wages. A higher union density is associated with lower residual wage dispersion, reduced skill wage differentials, and a lower wage level. This finding is in line with an insurance motive for union action. The thesis comprises the following articles: (1) “Rising Wage Dispersion, After All! The German Wage Structure at the Turn of the Century,” IZA Discussion Paper 2098, April 2006. (2) “Skill Wage Premia, Employment, and Cohort Effects: Are Workers in Germany All of the Same Type?”, IZA Discussion Paper 2185, June 2006, joint with Bernd Fitzenberger. (3) “The Erosion of Union Membership in Germany: Determinants, Densities, Decompositions,” IZA Discussion Paper 2193, July 2006, joint with Bernd Fitzenberger and Qingwei Wang. (4) “Equal Pay for Equal Work? On Union Power and the Structure of Wages in West Germany, 1985–1997,” translation of “Gleicher Lohn für gleiche Arbeit? Zum Zusammenhang zwischen Gewerkschaftsmitgliedschaft und Lohnstruktur in Westdeutschland 1985–1997,” Zeitschrift für Arbeitsmarkt-Forschung, 38 (2/3), 125-146, joint with Bernd Fitzenberger, 2005.
1 Purpose of the Study:
The purpose of this retrospective study was to assess the volumetric changes of our institutional pediatric neuroblastoma in response to various therapeutic protocols.
2 Materials and Methods:
A retrospective study was conducted on children with neuroblastoma from different anatomical locations including suprarenal, paraspinal, pelvic, mediastinal and cervical neuroblastoma primaries. These children underwent tumor-stage based therapeutic protocols in Johann Wolfgang Goethe University Hospital, Frankfurt am Main, Germany, between January 1996 and July 2008. The study included 72 patients (44 males and 28 females). Patient demographics (age and gender), disease-related symptoms, laboratory results (tumor biomarkers including ferritin, neuron specific enolase, and urine catecholamine) and histopathological reports were collected from the electronic medical archiving system and subsequently analyzed.
Patients were classified into following groups according the anatomical origin of the primary neuroblastoma into:
1) Suprarenal neuroblastoma Group: This group included patients with neuroblastoma arising from the suprarenal gland. This group composed of 54 patients with male to female ratio (32:22).
2) Paravertebral neuroblastoma Group: This group composed of 6 male patients.
3) Mediastinal neuroblastoma Group: This group included patients with mediastinal neuroblastoma and composed of 3 patients (1 male and 2 females).
4) Pelvic neuroblastoma Group: This group included patients with pelvic neuroblastoma and composed of 6 patients (3 males and 3 females).
5) Cervical neuroblastoma Group: This group included patients with cervical neuroblastoma and composed of 2 male patients.
3 Results:
The mean volume of all suprarenal neuroblastoma group involved in the study before therapy was 176.62 cm3 (SD: 234.15) range: 239.4-968.9cm3. The mean initial volume of all suprarenal neuroblastoma group who underwent observation protocol was 86.0378 cm3 (SD: 114.44) range: 5.2-347.94cm3. Volumetric evaluation of suprarenal neuroblastoma following observation (Wait and See) protocol revealed continuous reduction of the tumor volumes in a statistically significant manner during the follow up periods up to 12 months with p value of less than 0.05. The volumetric changes afterwards were statistically insignificant.
The mean initial volume of all suprarenal neuroblastoma group who underwent primary surgery protocol was 42.4 cm3 (SD: 28.5) range: 7.5-90cm3. Complete surgical resection of the tumor was not feasible in all lesions due to local tumor extension and / or infiltration with the associated risk of injury of nearby organs or structures. However statistical analysis of the volumetric changes in the successive follow up periods did not reveal statistical significance.
Volumetric estimation of the tumor in the subsequent follow up periods revealed significant changes within the period first (3-9 month periods). The changes afterwards were statistically non significant. On the other hand, the mean initial volume of all suprarenal neuroblastoma group who underwent combined chemotherapy and Stem cell transplantation protocol only without surgical interference was 99.98cm3 (SD:46.2) range: 48.48-160.48 cm3. In this group the volumetric changes were variable and difference in volumes in follow up was statistically non significant during the follow up period.
The mean initial volume of all abdominal paravertebral neuroblastoma group was 249.197cm3 (SD: 249.63) range: 9.6-934cm3. The mean initial volume of all pelvic neuroblastoma group was 118.88cm3 (SD: 50.61) range: 73.4-173.4cm3. The mean initial volume of all mediastinal neuroblastoma group was 189.7cm3 (SD: 139.057) range: 10.7-415 cm3. The mean initial volume of all cervical neuroblastoma group was 189.7cm3 (SD: 139.057) range: 10.7-415 cm3. The volumetric measurements in the corresponding follow up periods according to the therapeutic protocol of abdominal paravertebral neuroblastoma, pelvic neuroblastoma, mediastinal and cervical neuroblastoma revealed significant change in the tumor volume within the early 3-6 months from the initial therapy while subsequently the tumor volumetric changes were statistically non significant.
4 Conclusion:
In conclusion, the role of MRI volumetry in the evaluation of tumor response is dependent on the risk adapted concept of neuroblastoma with the combination of different imaging modalities as well the therapeutic protocol. MRI Volumetry in addition to new protocols such as Whole-body imaging and 3D visualization techniques are gaining more importance and acceptance.
This thesis investigates the structure of the translocase of the outer membrane (TOM) complex in mitochondria, focusing on the TOM holo complex through single-particle electron cryo-microscopy (cryoEM) complemented by mass spectrometry and computational structure prediction. Mitochondria, crucial for energy production in eukaryotic cells, import most of their proteins from the cytoplasm. These proteins enter through the TOM complex, which in its core form consists of a membrane-embedded homodimer of Tom40 pores, two Tom22 cytoplasmic receptors, and six small TOM stabilizing subunits (Tom7, Tom6, and Tom5). The holo complex includes two additional subunits, Tom70 and Tom20, whose stoichiometry and positioning are less understood due to their easy dissociation during isolation of the complex. CryoEM analysis revealed the high-resolution structure of the Neurospora crassa TOM core complex at 3.3 Å, containing all core subunits, and the presence of a central phospholipid causing the Tom40 dimer to tilt to 20°. Furthermore, a 4 Å resolution map indicated the binding of a precursor protein as it transitions through the translocation barrel. Finally, at 6-7 Å resolution, the structure of the TOM holo complex highlighted Tom20's flexibility as it interacts with the core complex, emphasizing its role in protein translocation. This work provides significant insights into the architecture and functioning of the TOM complex, contributing to the understanding of mitochondrial protein import mechanisms.
Through an examination of Joseph Roth’s reportage and fiction published between 1923 and 1932, this thesis seeks to provide a systematic analysis of a particular aspect of the author’s literary style, namely his use of sharply focused visual representations, which are termed Heuristic Visuals. Close textual analysis, supplemented by insights from reader-response theory, psychology, psycholinguistics and sociology illuminate the function of these visual representations. The thesis also seeks to discover whether there are significant differences and correspondences in the use of visual representations between the reportage and fiction genres. Roth believed that writers should be engagiert, and that the truth could only be arrived at through close observation of reality, not subordinated to theory. The research analyses the techniques by which Roth challenges his readers and encourages them to discover the truth for themselves. Three basic variants of Heuristic Visuals are identified, and their use in different contexts, including that of dialectical presentations, is explored. There is evidence of the use of different variants of Heuristic Visuals according to the respective rhetorical demands of particular thematic issues. It has also been possible to establish synchronic correspondences between the different genres, and diachronic correspondences within genres. Although there are examples within the reportage where the entire article is based on an Heuristic Visual, the use of Heuristic Visuals cannot be seen as a key organizing principle in Roth’s work as a whole. As his mastery of the technique reaches its highest point in the early 1930s, Heuristic Visuals are often incorporated into the reconstruction of a complete sensory experience. Analysis of Roth’s heuristic use of visual representations has led to important insights, including a reinterpretation of the endings of Roth’s two most famous novels: Hiob and Radetzkymarsch.
Virtuous democrats, liberal aristocrats : political discourse and the Pennsylvania Constitution
(2001)
Virtual screening of potential bioactive substances using the support vector machine approach
(2005)
Die vorliegende Dissertation stellt eine kumulative Arbeit dar, die in insgesamt acht wissenschaftlichen Publikationen (fünf publiziert, zwei eingerichtet und eine in Vorbereitung) dargelegt ist. In diesem Forschungsprojekt wurden Anwendungen von maschinellem Lernen für das virtuelle Screening von Moleküldatenbanken durchgeführt. Das Ziel war primär die Einführung und Überprüfung des Support-Vector-Machine (SVM) Ansatzes für das virtuelle Screening nach potentiellen Wirkstoffkandidaten. In der Einleitung der Arbeit ist die Rolle des virtuellen Screenings im Wirkstoffdesign beschrieben. Methoden des virtuellen Screenings können fast in jedem Bereich der gesamten pharmazeutischen Forschung angewendet werden. Maschinelles Lernen kann einen Einsatz finden von der Auswahl der ersten Moleküle, der Optimierung der Leitstrukturen bis hin zur Vorhersage von ADMET (Absorption, Distribution, Metabolism, Toxicity) Eigenschaften. In Abschnitt 4.2 werden möglichen Verfahren dargestellt, die zur Beschreibung von chemischen Strukturen eingesetzt werden können, um diese Strukturen in ein Format zu bringen (Deskriptoren), das man als Eingabe für maschinelle Lernverfahren wie Neuronale Netze oder SVM nutzen kann. Der Fokus ist dabei auf diejenigen Verfahren gerichtet, die in der vorliegenden Arbeit verwendet wurden. Die meisten Methoden berechnen Deskriptoren, die nur auf der zweidimensionalen (2D) Struktur basieren. Standard-Beispiele hierfür sind physikochemische Eigenschaften, Atom- und Bindungsanzahl etc. (Abschnitt 4.2.1). CATS Deskriptoren, ein topologisches Pharmakophorkonzept, sind ebenfalls 2D-basiert (Abschnitt 4.2.2). Ein anderer Typ von Deskriptoren beschreibt Eigenschaften, die aus einem dreidimensionalen (3D) Molekülmodell abgeleitet werden. Der Erfolg dieser Beschreibung hangt sehr stark davon ab, wie repräsentativ die 3D-Konformation ist, die für die Berechnung des Deskriptors angewendet wurde. Eine weitere Beschreibung, die wir in unserer Arbeit eingesetzt haben, waren Fingerprints. In unserem Fall waren die verwendeten Fingerprints ungeeignet zum Trainieren von Neuronale Netzen, da der Fingerprintvektor zu viele Dimensionen (~ 10 hoch 5) hatte. Im Gegensatz dazu hat das Training von SVM mit Fingerprints funktioniert. SVM hat den Vorteil im Vergleich zu anderen Methoden, dass sie in sehr hochdimensionalen Räumen gut klassifizieren kann. Dieser Zusammenhang zwischen SVM und Fingerprints war eine Neuheit, und wurde von uns erstmalig in die Chemieinformatik eingeführt. In Abschnitt 4.3 fokussiere ich mich auf die SVM-Methode. Für fast alle Klassifikationsaufgaben in dieser Arbeit wurde der SVM-Ansatz verwendet. Ein Schwerpunkt der Dissertation lag auf der SVM-Methode. Wegen Platzbeschränkungen wurde in den beigefügten Veröffentlichungen auf eine detaillierte Beschreibung der SVM verzichtet. Aus diesem Grund wird in Abschnitt 4.3 eine vollständige Einführung in SVM gegeben. Darin enthalten ist eine vollständige Diskussion der SVM Theorie: optimale Hyperfläche, Soft-Margin-Hyperfläche, quadratische Programmierung als Technik, um diese optimale Hyperfläche zu finden. Abschnitt 4.3 enthält auch eine Diskussion von Kernel-Funktionen, welche die genaue Form der optimalen Hyperfläche bestimmen. In Abschnitt 4.4 ist eine Einleitung in verschiede Methoden gegeben, die wir für die Auswahl von Deskriptoren genutzt haben. In diesem Abschnitt wird der Unterschied zwischen einer „Filter“- und der „Wrapper“-basierten Auswahl von Deskriptoren herausgearbeitet. In Veröffentlichung 3 (Abschnitt 7.3) haben wir die Vorteile und Nachteile von Filter- und Wrapper-basierten Methoden im virtuellen Screening vergleichend dargestellt. Abschnitt 7 besteht aus den Publikationen, die unsere Forschungsergebnisse enthalten. Unsere erste Publikation (Veröffentlichung 1) war ein Übersichtsartikel (Abschnitt 7.1). In diesem Artikel haben wir einen Gesamtüberblick der Anwendungen von SVM in der Bio- und Chemieinformatik gegeben. Wir diskutieren Anwendungen von SVM für die Gen-Chip-Analyse, die DNASequenzanalyse und die Vorhersage von Proteinstrukturen und Proteininteraktionen. Wir haben auch Beispiele beschrieben, wo SVM für die Vorhersage der Lokalisation von Proteinen in der Zelle genutzt wurden. Es wird dabei deutlich, dass SVM im Bereich des virtuellen Screenings noch nicht verbreitet war. Um den Einsatz von SVM als Hauptmethode unserer Forschung zu begründen, haben wir in unserer nächsten Publikation (Veröffentlichung 2) (Abschnitt 7.2) einen detaillierten Vergleich zwischen SVM und verschiedenen neuronalen Netzen, die sich als eine Standardmethode im virtuellen Screening etabliert haben, durchgeführt. Verglichen wurde die Trennung von wirstoffartigen und nicht-wirkstoffartigen Molekülen („Druglikeness“-Vorhersage). Die SVM konnte 82% aller Moleküle richtig klassifizieren. Die Klassifizierung war zudem robuster als mit dreilagigen feedforward-ANN bei der Verwendung verschiedener Anzahlen an Hidden-Neuronen. In diesem Projekt haben wir verschiedene Deskriptoren zur Beschreibung der Moleküle berechnet: Ghose-Crippen Fragmentdeskriptoren [86], physikochemische Eigenschaften [9] und topologische Pharmacophore (CATS) [10]. Die Entwicklung von weiteren Verfahren, die auf dem SVM-Konzept aufbauen, haben wir in den Publikationen in den Abschnitten 7.3 und 7.8 beschrieben. Veröffentlichung 3 stellt die Entwicklung einer neuen SVM-basierten Methode zur Auswahl von relevanten Deskriptoren für eine bestimmte Aktivität dar. Eingesetzt wurden die gleichen Deskriptoren wie in dem oben beschriebenen Projekt. Als charakteristische Molekülgruppen haben wir verschiedene Untermengen der COBRA Datenbank ausgewählt: 195 Thrombin Inhibitoren, 226 Kinase Inhibitoren und 227 Faktor Xa Inhibitoren. Es ist uns gelungen, die Anzahl der Deskriptoren von ursprünglich 407 auf ungefähr 50 zu verringern ohne signifikant an Klassifizierungsgenauigkeit zu verlieren. Unsere Methode haben wir mit einer Standardmethode für diese Anwendung verglichen, der Kolmogorov-Smirnov Statistik. Die SVM-basierte Methode erwies sich hierbei in jedem betrachteten Fall als besser als die Vergleichsmethoden hinsichtlich der Vorhersagegenauigkeit bei der gleichen Anzahl an Deskriptoren. Eine ausführliche Beschreibung ist in Abschnitt 4.4 gegeben. Dort sind auch verschiedene „Wrapper“ für die Deskriptoren-Auswahl beschrieben. Veröffentlichung 8 beschreibt die Anwendung von aktivem Lernen mit SVM. Die Idee des aktiven Lernens liegt in der Auswahl von Molekülen für das Lernverfahren aus dem Bereich an der Grenze der verschiedenen zu unterscheidenden Molekülklassen. Auf diese Weise kann die lokale Klassifikation verbessert werden. Die folgenden Gruppen von Moleküle wurden genutzt: ACE (Angiotensin converting enzyme), COX2 (Cyclooxygenase 2), CRF (Corticotropin releasing factor) Antagonisten, DPP (Dipeptidylpeptidase) IV, HIV (Human immunodeficiency virus) protease, Nuclear Receptors, NK (Neurokinin receptors), PPAR (peroxisome proliferator-activated receptor), Thrombin, GPCR und Matrix Metalloproteinasen. Aktives Lernen konnte die Leistungsfähigkeit des virtuellen Screenings verbessern, wie sich in dieser retrospektiven Studie zeigte. Es bleibt abzuwarten, ob sich das Verfahren durchsetzen wird, denn trotzt des Gewinns an Vorhersagegenauigkeit ist es aufgrund des mehrfachen SVMTrainings aufwändig. Die Publikationen aus den Abschnitten 7.5, 7.6 und 7.7 (Veröffentlichungen 5-7) zeigen praktische Anwendungen unserer SVM-Methoden im Wirkstoffdesign in Kombination mit anderen Verfahren, wie der Ähnlichkeitssuche und neuronalen Netzen zur Eigenschaftsvorhersage. In zwei Fällen haben wir mit dem Verfahren neuartige Liganden für COX-2 (cyclooxygenase 2) und dopamine D3/D2 Rezeptoren gefunden. Wir konnten somit klar zeigen, dass SVM-Methoden für das virtuelle Screening von Substanzdatensammlungen sinnvoll eingesetzt werden können. Es wurde im Rahmen der Arbeit auch ein schnelles Verfahren zur Erzeugung großer kombinatorischer Molekülbibliotheken entwickelt, welches auf der SMILES Notation aufbaut. Im frühen Stadium des Wirstoffdesigns ist es wichtig, eine möglichst „diverse“ Gruppe von Molekülen zu testen. Es gibt verschiedene etablierte Methoden, die eine solche Untermenge auswählen können. Wir haben eine neue Methode entwickelt, die genauer als die bekannte MaxMin-Methode sein sollte. Als erster Schritt wurde die „Probability Density Estimation“ (PDE) für die verfügbaren Moleküle berechnet. [78] Dafür haben wir jedes Molekül mit Deskriptoren beschrieben und die PDE im N-dimensionalen Deskriptorraum berechnet. Die Moleküle wurde mit dem Metropolis Algorithmus ausgewählt. [87] Die Idee liegt darin, wenige Moleküle aus den Bereichen mit hoher Dichte auszuwählen und mehr Moleküle aus den Bereichen mit niedriger Dichte. Die erhaltenen Ergebnisse wiesen jedoch auf zwei Nachteile hin. Erstens wurden Moleküle mit unrealistischen Deskriptorwerten ausgewählt und zweitens war unser Algorithmus zu langsam. Dieser Aspekt der Arbeit wurde daher nicht weiter verfolgt. In Veröffentlichung 6 (Abschnitt 7.6) haben wir in Zusammenarbeit mit der Molecular-Modeling Gruppe von Aventis-Pharma Deutschland (Frankfurt) einen SVM-basierten ADME Filter zur Früherkennung von CYP 2C9 Liganden entwickelt. Dieser nichtlineare SVM-Filter erreichte eine signifikant höhere Vorhersagegenauigkeit (q2 = 0.48) als ein auf den gleichen Daten entwickelten PLS-Modell (q2 = 0.34). Es wurden hierbei Dreipunkt-Pharmakophordeskriptoren eingesetzt, die auf einem dreidimensionalen Molekülmodell aufbauen. Eines der wichtigen Probleme im computerbasierten Wirkstoffdesign ist die Auswahl einer geeigneten Konformation für ein Molekül. Wir haben versucht, SVM auf dieses Problem anzuwenden. Der Trainingdatensatz wurde dazu mit jeweils mehreren Konformationen pro Molekül angereichert und ein SVM Modell gerechnet. Es wurden anschließend die Konformationen mit den am schlechtesten vorhergesagten IC50 Wert aussortiert. Die verbliebenen gemäß dem SVM-Modell bevorzugten Konformationen waren jedoch unrealistisch. Dieses Ergebnis zeigt Grenzen des SVM-Ansatzes auf. Wir glauben jedoch, dass weitere Forschung auf diesem Gebiet zu besseren Ergebnissen führen kann.
Time-critical applications process a continuous stream of input data and have to meet specific timing constraints. A common approach to ensure that such an application satisfies its constraints is over-provisioning: The application is deployed in a dedicated cluster environment with enough processing power to achieve the target performance for every specified data input rate. This approach comes with a drawback: At times of decreased data input rates, the cluster resources are not fully utilized. A typical use case is the HLT-Chain application that processes physics data at runtime of the ALICE experiment at CERN. From a perspective of cost and efficiency it is desirable to exploit temporarily unused cluster resources. Existing approaches aim for that goal by running additional applications. These approaches, however, a) lack in flexibility to dynamically grant the time-critical application the resources it needs, b) are insufficient for isolating the time-critical application from harmful side-effects introduced by additional applications or c) are not general because application-specific interfaces are used. In this thesis, a software framework is presented that allows to exploit unused resources in a dedicated cluster without harming a time-critical application. Additional applications are hosted in Virtual Machines (VMs) and unused cluster resources are allocated to these VMs at runtime. In order to avoid resource bottlenecks, the resource usage of VMs is dynamically modified according to the needs of the time-critical application. For this purpose, a number of previously not combined methods is used. On a global level, appropriate VM manipulations like hot migration, suspend/resume and start/stop are determined by an informed search heuristic and applied at runtime. Locally on cluster nodes, a feedback-controlled adaption of VM resource usage is carried out in a decentralized manner. The employment of this framework allows to increase a cluster’s usage by running additional applications, while at the same time preventing negative impact towards a time-critical application. This capability of the framework is shown for the HLT-Chain application: In an empirical evaluation the cluster CPU usage is increased from 49% to 79%, additional results are computed and no negative effect towards the HLT-Chain application are observed.
Autophagy, together with the ubiquitin-proteasome system, is the main quality control pathway responsible for maintaining cell homeostasis. There are several types of autophagy distinguished by cargo selectivity and means of induction. This thesis focuses on macroautophagy, hereafter autophagy, where a double-layered membrane is formed originating from the endoplasmatic reticulum (ER) engulfing cargo selectively or unselectively. Subsequently, a vesicle forms around the cargo, an autophagosome, and eventually fuses with the lysosome leading to degradation of the vesicle content and release of the cargo “building blocks”. Basal autophagy continuously occurs, unselectively engulfing a portion of the cytoplasm. However, autophagy can also be induced by stress such as starvation, protein aggregation, damaged organelles, intracellular pathogens etc. In this case, the cargo is selectively targeted, and the fate of the autophagosome is the same as in basal autophagy. In recent years, interest in identifying mechanisms of autophagy regulation has risen due to its importance in neurodegenerative diseases and cancer. Given the complexity of the process, its execution is tightly regulated from initiation, autophagosome formation, expansion, closure, and finally fusion with the lysosome. Each of the steps involves different protein complexes, whose timely activity is orchestrated by post-translational modifications. One of them is ubiquitination. Ubiquitin is a small, 76-amino acid protein conjugated in a 3-step reaction to other proteins, in a reversible manner, meaning undone by deubiquitinases. Originally described as a degradation signal targeting proteins to the proteasome, today it is known it has various additional non-proteolytic functions, such as regulating a protein’s activity, localization, or interaction partners. The role of ubiquitin in autophagy has already been shown. However, given the reversibility and fine-tuning of the ubiquitin signal, many expected regulators remain unidentified. This work aimed to identify novel deubiquitinating enzymes that regulate autophagy. We identified ubiquitin-specific protease 11 (USP11) as a novel, negative regulator of autophagy. Loss of USP11 leads to an increase in autophagic flux, whereas overexpression of USP11 attenuates it. Moreover, this observation was reproducible in model organism Caenorhabditis elegans, emphasizing the importance of USP11 in autophagy regulation. To identify the mechanism of USP11-dependent autophagy regulation, we performed a USP11 interactome screen after 4 hour Torin1 treatment and identified a plethora of autophagy-related proteins. Following the most prominent hits, we have investigated versatile ways in which USP11 regulates autophagy. USP11 interacts with the PI3KC3 complex, the role of which is phosphorylating lipids of the ER, thereby initiating the formation of the autophagosomal membrane. Phosphorylated lipids serve as a recruitment signal for downstream effector proteins necessary for the membrane expansion. The core components of the complex are VPS34, the lipid kinase, ATG14, the protein responsible for targeting the complex to the ER, VPS15, a pseudokinase with a scaffolding role, Beclin1, a regulatory subunit, and NRBF2, the dimer-inducing subunit. We have found USP11 interacts with the complex and, based on its activity, USP11 influences post-translational status of all the aforementioned subunits, except for ATG14. Moreover, we have found that loss of USP11 leads to an increase in NRBF2 levels, whereas it does not change the levels of the other proteins. Given that the dimerization of the complex leads to an increase in complex activity, we investigated if the complex is more tightly formed in the absence of USP11, and if it is more active. We have found both to be the case. Although the exact mechanism of USP11-dependent PI3KC3 complex regulation remains to be identified, we found that loss of USP11 stimulates the complex formation and activity, likely contributing to the general effect of USP11 on autophagy flux. Additionally, we found that USP11 modulates levels of mTOR, the most upstream kinase in autophagy initiation steps and general multifaceted metabolism regulator. Loss of USP11 led to downregulation of mTOR levels, suggesting USP11 may rescue mTOR from proteasome-mediated degradation. Furthermore, we found mTOR to be differentially modified depending on the activity of USP11. However, it remains to be shown if USP11-dependent mTOR regulation contributes to the observed autophagy phenotype. Taken together, USP11 is a novel, versatile, negative regulator of autophagy, and an important addition to our knowledge on the regulation of autophagy by the ubiquitin system.
With the increasing energies and intensities of heavy-ion accelerator facilities, the problem of an excessive activation of the accelerator components caused by beam losses becomes more and more important. Numerical experiments using Monte Carlo transport codes are performed in order to assess the levels of activation. The heavy-ion versions of the codes were released approximately a decade ago, therefore the verification is needed to be sure that they give reasonable results. Present work is focused on obtaining the experimental data on activation of the targets by heavy-ion beams. Several experiments were performed at GSI Helmholtzzentrum für Schwerionenforschung. The interaction of nitrogen, argon and uranium beams with aluminum targets, as well as interaction of nitrogen and argon beams with copper targets was studied. After the irradiation of the targets by different ion beams from the SIS18 synchrotron at GSI, the γ-spectroscopy analysis was done: the γ-spectra of the residual activity were measured, the radioactive nuclides were identified, their amount and depth distribution were detected. The obtained experimental results were compared with the results of the Monte Carlo simulations using FLUKA, MARS and SHIELD. The discrepancies and agreements between experiment and simulations are pointed out. The origin of discrepancies is discussed. Obtained results allow for a better verification of the Monte Carlo transport codes, and also provide information for their further development. The necessity of the activation studies for accelerator applications is discussed. The limits of applicability of the heavy-ion beam-loss criteria were studied using the FLUKA code. FLUKA-simulations were done to determine the most preferable from the radiation protection point of view materials for use in accelerator components.
The venture capital industry holds relevance for entrepreneurs looking for money to finance an innovative project, investors seeking to make money by investing in entrepreneurial firms and governments trying to promote innovation and entrepreneurship. Venture capital investment could facilitate innovation and thus a better economy.
Venture capital has enabled the U.S. to support its entrepreneurial talent by turning ideas into world-famous products and services, building companies from mere business plans to mature and powerful organizations. Three of the five largest U.S. public companies by market capitalization – Apple, Google and Microsoft – received most of their early external funding from venture capital. Having its ups and downs, venture capital investment in the U.S. expanded from virtually zero in the mid-1970s to $8 billion in 1995 and $49.3 billion in 2014. Venture backed companies have been a prime driver of economic growth in the U.S.Across the pacific, venture capital investment in China has grown out of the transition from a centrally planned economy to a free market economy over the past three decades, becoming an important pillar supporting China’s innovation system. In 2015, a total of 2,824 venture capital investment deals provided an aggregate investment of $36.9 billion. Venture capital has long been a hot topic in China’s capital market, particularly since the government decided to boost “mass entrepreneurship and innovation” in 2014.
In the U.S., most venture capital firms are organized as limited partnerships, with the venture capitalists being general partners and the investors limited partners. Studies have shown that investors choose to invest through venture funds as an intermediary rather than placing their investments directly with the entrepreneurs; because of the high risk nature of the entrepreneur’s business, it is hard for them to get bank loans or direct equity investments. Conflicts may also arise, however, between the venture capitalists acting as agents and the investors as principals.5 This agency problem maybe particularly severe, since venture capital provides money for businesses with high potential and high risk, although the limited partnership has certain merits and is still most commonly chosen as the business form for venture capital funds.6 At the same time, the fact that general partners have total control of the partnership business necessitates that the agency problem is addressed by legal rules, contracts and other mechanisms.
Meanwhile, despite the rapid growth of venture capital investments in China, little attention has been paid to the organizational form of venture capital funds. In contrast to the U.S., most Chinese venture funds have been structured as corporations. One may argue that it was due to legislative reasons: that the limited partnership was not recognized by Chinese law when venture capital first appeared in China. However, after adopted a chapter was adopted in the Partnership Enterprise Law (PEL) governing limited partnerships in 2007, most of the venture funds abided by their choice, while those opting for the limited partnership have encountered difficulties: the limited partners are having trouble trusting the general partners with their money and are therefore interfering with the operation of the partnership business, which may lead to dissolution of the partnership.
This thesis applies transaction cost theory to explain the benefits and costs of choosing the limited partnership as a business form in the special context of venture capital investments, showing that the potential agency conflict between the general partners and the limited partners have been mitigated by legal and other mechanismsin the United States, and that the U.S. investors could therefore exploit the merit of the limited partnership form in venture capital financing. In China, investors have different answers to the agency problem. Similarly to the situation in the U.S., Chinese partners also employ contract terms to deal with agency problems, and the legislators enact laws that aim at regulating the limited partnership form; some legislation was even transplanted from the U.S., such as that part of the PEL which governs limited partnerships. It seems, then, that similar mechanisms that deal with agency problems also exist in China. However, given the unique history of the development of China’s innovation system and venture capital market, the effectiveness of these constraints is questionable. Chinese venture capital investors have therefore characteristically behaved differently to U.S. investors. Rather than relying on these questionable mechanisms, Chinese investors as well as the Chinese government have developed different approaches to addressing these agency problems.
Snake bite envenoming often results in disability or death of breadwinners of poor families in the rural tropics and the subtropics of Nepal. Identification of the medically relevant snake species, circumstances of venomous snake bites, prehospital care of their bites and human responses to snakes and snake bite is, therefore, crucial to enable victims or first aider to select the appropriate first aid measures, physicians to anticipate complications and to use appropriate treatment protocols as well as the local community to implement prevention strategies. Inadequate educational gaps exist in Nepal and hinder identification of snakes involved in bites. To fill this gap, I aim to provide an evidence-based list of medically relevant snake species. Snake specimens brought by patients bitten or their attendants from the tropical and subtropical regions in southeastern, southcentral, and southwestern Nepal to snake bite treatment centres over a period from 2010 through 2014, were taxonomically identified and medical records of envenoming were evaluated.
In Nepal, the epidemiology of snake bite is poorly known. Here I describe the ecological circumstances of proven krait (Bungarus spp.) and Russell´s Viper (Daboia russelii) bites to elucidate and examine, whether environmental circumstances or human behaviour contributed to envenoming. In a cross-sectional study, data about prehospital care, environmental circumstances of 46 krait and 10 Russell´s Viper bites were evaluated. Patients were interviewed using structured interview forms. Snake bite prone communities were surveyed to test people´s knowledge on snakes and their attitude towards venomous snakes in general.
Of 349 snakes involved in bites, 199 (57%) specimens were found to be medically relevant venomous snakes that included 11 species belonging to six genera and two families. Among them, Naja naja (n = 76, 22%), Bungarus caeruleus (n = 65, 19%) and Trimeresusurs albolabris (n = 10, 3%) were the most widely distributed snakes. Daboia russelii (n = 10, 3%) was found to be restricted to the southwestern part of Nepal. For B. walli, a previously poorly known species, 13 voucher specimens represent the first country records of this species as well as the first documented cases of involvement in snake bite envenoming by this species in Nepal.
Numerous snake bites (33%) occurred at night, during the rainy season, and are mainly due to Bungarus species, particularly B. caeruleus. Bites of cobras and Russell’s Vipers are a risk at daytime. Evaluation of data regarding the place where the bite happened, indicates that the snake bite risks appear to be as high in residential areas, in and around houses, as in rural areas. In cases of kraits (n = 46), 61% of the bites occurred while the victim was sleeping indoors, those of Russell´s Vipers mainly during agricultural activities in the fields. Analysis of socio-demographic data revealed that both krait and viper bites predominantly affected farmers or their family members. However, snake bites involved also people of higher socio-economic status, which suggests that it is not a health problem of poor people only living in the rural areas of Nepal.
A small number of snake bite victims (n = 7) sought help from traditional healers, but most patients went to hospitals for medical treatment using motorbikes (65%) or were transferred by ambulance cars (22%). As a first aid measure, most patients (78%) had used a tourniquet, which is of doubtful value and has often severe sequelae, instead of applying the WHO recommended pressure immobilisation bandage or local compression pad. The overall case fatality rate was calculated to be 10%, but up to 17% in cases of Bungarus spp. bites.
Rural community people were found to be extremely afraid of snakes, a major reason for indiscriminate killing of even harmless snakes, e.g., Lycodon aulicus, which were wrongly considered to be venomous. This is mainly due to the poor knowledge on snakes in general and on their role in providing ecological services, which may eventually lead to a decline in snake populations and even the extinction of rare species.
The results of the present study strongly emphasize that snake bite is an important public health issue in Nepal. There is an urgent need to improve the knowledge of people on snakes and to try changing their attitudes towards these reptiles, in addition to documenting the biodiversity and distribution of medically relevant snakes, the epidemiology and circumstances of their bites. Avoiding high-risk behaviour (e.g., killing of snakes), using screened doors and windows are some of the suggested measures preventing snake bite. Early and accurate identification of the snakes involved should help physicians to apply timely treatment, eventually referring the patient to the appropriate hospital. This also has important implications in developing public health and conservation strategies, to the benefit of the people of Nepal.
Savannas provide essential ecosystem services for human well-being in West Africa. Thus, ecosystem change not only directly affects biodiversity but also human livelihoods. Human land use considerably shaped these savanna ecosystems for millennia, particularly agriculture, livestock grazing, logging and the collection of non-timber forest products (NTFPs). NTFPs are wild plant products and comprise all organic matter from herbaceous plants, shrubs, and trees (excluding timber). Current increasing land use pressure through fast demographic changes is widely esteemed as a severe threat for savanna biodiversity and the socio-economy of rural communities. In consideration of the pivotal role of NTFP species for biodiversity and livelihoods, it is important to evaluate the effect of increasing land use change on savanna vegetation and on its provisioning service for human well-being. Thus, the major aim of this thesis is to investigate the impacts of land use intensification on vegetation composition, diversity and function and its consequences for provisioning ecosystem services (NTFPs) and human well-being in a West African savanna.
The research for this study was conducted in the North Sudanian vegetation zone of south-eastern Burkina Faso, where population growth exceeds the nationwide trend. Generally, Burkina Faso belongs to the worldwide poorest countries, where nearly one quarter of the population suffers from malnutrition (FAO 2014). The integration of NTFPs and particularly wild food species into rural household economies is, thus, an important measure in the national combat against poverty and food insecurity (FAO 2014). Against this background, I focus on vegetation changes, the economic importance of NTFPs as well as the decrease and substitution of wild food species in this study.
Vegetation resurveys of different vegetation types since the early 1990s showed that land use change led to more pronounced changes in the herbaceous than in the woody vegetation layer. Most woody vegetation types stayed stable in species composition and richness, even though some highly useful tree species (Vitellaria paradoxa, Parkia biglobosa) declined in some woody vegetation types. In contrast, in most herbaceous vegetation types species richness increased and species composition considerably changed. This change might be explained by a general ruderalisation process through a pronounced increase of wide-ranging herbaceous species. However, in spite of a general species increase in the herbaceous layer, a decrease of preferred herbaceous fodder species was found. Thus, the decline of useful species in both layers is alarming. Herbaceous vegetation types also showed more pronounced changes in plant functional trait characteristics in comparison to woody vegetation types. However, an increase of smaller plant species and species with a high diaspore terminal velocity (VTerm) was found in both vegetation layers. Since these two trait responses are generally related to grazing and browsing, the strong increase of livestock herds is likely to be responsible for the detected vegetation changes.
In addition to the vegetation study, interviews showed that all useful food species were widely considered to decline. The two economically most important tree species, the shea tree (Vitellaria paradoxa) and the locust bean tree (Parkia biglobosa) that contribute with 70% to wild food income, were considered among the most declining species of all cited wild food species. On this matter, local perceptions of species decline and results from field observations are in accordance. However, a wide range of cited substitutes indicated a great knowledge on alternative plant species in the area. Most wild food species are, however, substituted by other highly valued wild food species. Although our results suggest that rural communities are able to cope with the decrease or absence of wild food species, growing decline of one species would concurrently increase the pressure on other native food species. Therefore, the need to counteract the decrease of highly useful wild food species should be of high priority in management measures. In general, I showed that NTFPs are an essential component in rural households, since it contributed with 45 % to total household income. Significant differences in NTFP dependency between the two investigated villages and across the three main ethnic groups were detected, reflecting different traditional uses and harvesting practices. In general, it was shown that poorer households depend more on NTFP income than wealthier households. Against the background of this study, management strategies for agroforestry systems and poverty alleviation should consider local differences, and ethnicity-dependent NTFP-use patterns.
Overall, the combination of field studies on temporal and functional vegetation change with socio-economic and ethno-botanic interviews increases the knowledge on qualitative and quantitative vegetation changes and on the consequences for rural populations. This thesis gives a thorough insight into decreasing trends of economically valued plant species and thus gives evidence on the consequences of vegetation changes for ecosystem services of West African savanna ecosystems. Further, different NTFP-dependencies and use preferences according to socio-economic and cultural variables, such as ethnicity, present a valuable basis for specific decision-making and should be considered in management plans.
Die vorliegende Arbeit beschäftigt sich mit der BFV-Reduktion von Hamiltonschen Systemen mit erstklassigen Zwangsbedingungen im Rahmen der klassischen Hamiltonschen Mechanik und im Rahmen der Deformationsquantisierung. Besondere Aufmerksamkeit wird dabei Zwangsbedingungen zuteil, die als Nullfaser singulärer äquivarianter Impulsabbildungen entstehen. Es ist schon länger bekannt, daß für Nullfasern regulärer äquivarianter Impulsabbildungen die in der theoretischen Physik gebräuchliche Methode der BFV-Reduktion zur Phasenraumreduktion nach Marsden/Weinstein äquivalent ist. In [24] konnte gezeigt werden, daß in dieser Situation die BFV-Reduktion sich auch im Rahmen der Deformationsquantisierung natürlich formulieren läßt und erfolgreich zur Konstruktion von Sternprodukten auf Marsden/Weinstein-Quotienten verwendet werden kann. Ein Hauptergebnis der vorliegenden Arbeit besteht in der Verallgemeinerung der Ergebnisse aus [24] auf den Fall singulärer Impulsabbildungen, deren Komponenten 1.) das Verschwindungsideal der Zwangsfläche erzeugen und 2.) einen vollständigen Durchschnitt bilden. Die Argumentation von [24] wird durch Gebrauch der Störungslemmata aus dem Anhang A.1 systematisiert und vereinfacht. Zum Existenzbeweis von stetigen Homotopien und stetiger Fortsetzungsabbildung für die Koszulauflösung werden der Zerfällungssatz und der Fortsetzungssatz von Bierstone und Schwarz [20] benutzt. Außerdem wird ein ’Jacobisches Kriterium’ für die Überprüfung von Bedingung 2.) angegeben. Basierend auf diesem Kriterium und Techniken aus [3] werden die Bedingungen 1.) und 2.) an einer Reihe von Beispielen getestet. Als Korollar erhält man den Beweis dafür, daß es symplektisch stratifizierte Räume gibt, die keine Orbifaltigkeiten sind und dennoch eine stetige Deformationsquantisierung zulassen. Ferner wird (ähnlich zu [92]) eine konzeptionielle Erklärung dafür gegeben, warum im Fall vollständiger Durchschnitte das Problem der Quantisierung der BRST-Ladung eine so einfache Lösung hat. Bildet die Impulsabbildung eine erstklassige Zwangsbedingung, ist aber kein vollständiger Durchschnitt, dann ist es im allgemeinen nicht bekannt, wie entsprechende Quantenreduktionsresultate zu erzielen sind. Ein Hauptaugenmerk der Untersuchung wird es deshalb sein, in dieser Situation die klassische BFV-Reduktion besser zu verstehen – natürlich in der Hoffnung, Grundlagen für eine etwaige (Deformations-)Quantisierung zu liefern. Wir werden feststellen, daß es zwei Gründe gibt, die Tate-Erzeuger (alias: Antigeister höheren Niveaus) notwendig machen: die Topologie der Zwangsfläche und die Singularitätentheorie der Impulsabbildung. Die Zahl der Tate-Erzeuger kann durch Übergang zu projektiven Tate-Erzeugern, also Vektorbündeln, verringert werden. Allerdings sorgt Halperins Starrheitssatz [57] dafür, daß im wesentlichen alle Fälle, für die die Zwangsfläche kein lokal vollständiger Durchschnitt ist, zu unendlich vielen Tate-Erzeugern führen. Erzeugen die Komponenten einer Impulsabbildung einer linearen symplektischen Gruppenwirkung das Verschwindungsideal der Zwangsfläche, so kann man eine lokal endliche Tate-Auflösung finden. Diese besitzt nach dem Fortsetzungssatz und dem Zerfällungssatz von Bierstone und Schwarz stetige, kontrahierende Homotopien. Ausgehend von einer solchen Tate-Auflösung konstruieren wir, die klassische BFV-Konstruktion für vollständige Durchschnitte verallgemeinernd, eine graduierte superkommutative Algebra. Wir können zeigen, daß diese graduierte Algebra auch im Vektorbündelfall eine graduierte Poissonklammer besitzt, die sogenannte Rothstein-Poissonklammer. Die Existenz einer solchen Poissonklammer war bereits von Rothstein [87] für die einfachere Situation einer symplektischen Supermannigfaltigkeit bewiesen worden. Darüberhinaus werden wir sehen, daß es auch im Vektorbündelfall eine BRST-Ladung gibt. Diese sieht im Fall von Impulsabbildungen etwas einfacher aus als für allgemeine erstklassige Zwangsbedingungen. Insgesamt wird also die klassische BFV-Konstruktion [95] auf den Fall projektiver Tate-Erzeuger verallgemeinert, und als eine Homotopieäquivalenz in der additiven Kategorie der Fréchet-Räume interpretiert.
This research investigated variation in the pronunciations of three RP vowels phonemes /e/, /ɜ:/ and /ə/, among Ewe speakers of English in Ghana. It focused on variation at both individual and societal levels, investigating how social relations within these structures influenced the use of the three vowels among the speakers. In this study, social structures were seen as a system where individual members depended on one another and were linked through multiple ties. The distribution of the vowels was in respect with the social variables: age, gender and education, including dialect and social network. The study used a corpus of word-list recorded in a face-to-face interview from 96 participants selected through stratification and networking across two dialect regions: Aŋlɔ and Eveme. Using both aural and acoustic analyses, coupled with ANOVA and t-test, the study has shown that the three RP vowels exist in Ghana Eve English as independent phonemes. Each of them however has allophonic variants; /e/ has variants [e̠], [ɪ] and [ɜ:]; /ɜ:/ has [eː] and [ɜ:], while /ə/ has [ə], [ɪ], [o] and [ʌ] as its variants. The choice of the variants of /ɜ:/ and /e/ have been found to depend on speaker age, gender, and social network. But the geographical location of the speaker will largely determine how these vowels are spoken. Phonological contexts as well as speaker idiosyncrasy are also likely to condition the choice of some of these variants, however, their effects seem less important as determinant of the differences observed than those of the social factors. It is evident that age, gender and class differentiations that have been widely reported cannot be universal, they can vary from one society to another. Also though social structures as well as social relations in a speech community can play significant roles in the individual’s linguistic repertoire, the attitude of the speaker and the phonological contexts of a segment can have a huge impact on the use of that variable.
Variation in enclitic possessive constructions in Southern Italian dialects: a syntactic analysis
(2019)
This thesis investigates enclitic possessive constructions (EPCs) that are a widespread and frequently used construction among Southern Italian dialects (SIDs). In general, EPCs display the structure N-EP where the N is a (singular) kinship noun and the EP the enclitic possessive directly attached to the kinship noun. However, there is a huge variation among SIDs as well as within the system of a specific dialect. The aim of the present work is twofold. The empirical part contributes new data to this topic as well as a detailed and organized overview of (micro-) variational observations from data of different sources including for example the linguistic maps of the AIS (Atlante Italo-Svizzero). The main aspects of variation are (a) the presence or absence of an obligatory article (D – N-EP vs. N-EP), (b) the possibility of plural kinship noun-EPCs and (c) the compatibility of a specific person-EP with a specific kinship noun within a dialect. Based on the empirical findings, the syntactic part proposes a syntactic analysis for EPCs focusing on the following research questions: 1) In some dialects, singular kinship noun-EPCs display an obligatory article with the 3SG.EP. What is the reason for this article-based person split (1st and 2nd vs. 3rd)? And further, how are both structures, with and without an article, represented in the syntax, i.e. in DP and PossP? 2) In some dialects, plural kinship nouns are allowed to occur in EPCs, and in others, they are disallowed. With respect to this dichotomy, what is the role of NumP? 3) Kinship nouns are relational and express inalienability. How can this property be captured in the syntax? I argue that the article-based person split is due to the deictic properties of the possessor-persons, meaning that 1SG.EPs and 2SG.EPs need to be bound by the speaker’s coordinates in the left periphery of the clause, whereas 3SG.EPs do not. As a consequence, 1SG and 2SG EPCs move to the highest position, i.e. to D°, and 3SG EPCs can stay lower in the structure, i.e. in Poss°. Based on this dichotomy, I argue that both D° and Poss° can host EPCs. In order to capture the (im)possibility of plural kinship nouns-EPCs, I argue that NumP, as a parametrised position, can block or allow further movement of the kinship noun to Poss° (and to D°). With respect to the relational nature of kinship nouns I propose that they are base-generated within the complement position of a relator phrase (RP), and EPs in Poss°. In order to derive EPCs, the kinship nouns must move out of their position. The kinship noun lands in NumP, the position where further movement is probably blocked. If further movement is allowed, the kinship noun merges to the left of the EP, resulting in a complete EPC in Poss°. The last leg of the movement to D° depends on the presence of absence of an obligatory article. The phenomenon of EPCs displays a huge variation among SIDs and needs to be investigated from different perspectives and different linguistic areas. The present work contributes to the puzzle of EPCs new data and a syntactic analysis.
This dissertation consists of three essays, which study the relation between stock prices and the macroeconomy using vector autoregressions (VARs). The first essay focuses on the link between stock prices and the current account. I find that stock markets provide a channel, in addition to the traditional exchange rate channel, through which external balance for a country with a current account imbalance can be restored. The second essay explores the transmission of U.S. stock price shocks to real activity and prices in G-7 countries. I achieve identification by imposing a small number of sign restrictions on impulse responses, while controlling for monetary policy, business cycle and government spending shocks. The results suggest that stock price movements are important for fluctuations in G-7 real activity and prices, but do not qualify as demand side business cycle shocks. The third essay investigates the impact of monetary and technology shocks on the stock market. I find an important role for technology shocks, but not monetary shocks, in explaining variations in real stock prices. The identification method is flexible enough to study the effects of technology news shocks. The responses are consistent with the idea that news on technology improvements have an immediate impact on stock prices.
Aim: To study the changes in leiomyoma volume following uterine artery embolization (UAE) and to correlate these changes with the initial leiomyoma volume and location within the uterus and to evaluate the impact of preprocedural prediction of the best tube angle obliquity for visualization of the uterine artery origin using 3D-reconstructed contrast-enhanced MR angiography (CE-MRA) on the radiation dose, fluoroscopy time and contrast medium volume used during UAE. Materials and Methods: The study was performed in two parts. The first part was retrospectively done on 28 patients (age range: 37-57 years, mean: 48 years, SD: 4.81) in whom UAE was performed. All leiomyomas in all patients were evaluated. In total, 84 leiomyomas were evaluated. MRI studies were performed before, 3 months and 1 year after UAE. The volumes and location of each leiomyoma in each patient were evaluated in consensus by two radiologists. The second part included 40 consecutive patients (age range: 37-56 years, mean: 46 years, SD: 4.49) and was done in a controlled prospective/retrospective manner. In 20 sample patients (prospective part) pre-procedural prediction of the best tube angle obliquity was predicted using 3D-reconstructed CE-MRA and provided to the interventionalist. 3D-reconstruction was done using Inspace application. The radiation dose, fluoroscopy time and contrast medium volume for those patients were compared with the data of the last 20 procedures (control) performed by the same interventionalist (retrospective part). Results: For the first part the mean pre-embolization volume was 51.6 cm3 range:0.72-371.1cm3, SD=79.3). At 3-month follow-up 83 (98.8%) leiomyomas showed a mean volume reduction of 52.62% (range: 12.79–96.67%, SD=21.85) and 1 leiomyoma (1.2%) increased in volume. At 1-year follow-up 5 (6%) leiomyomas were not detectable, 72 (85.7%) showed a further mean of 20.5% (range: 2.52–58.72%, SD=11.92) volume reduction compared to the 3-month follow-up volume and 7 (8.3%) leiomyomas increased in volume. A statistically significant (p=0.026 at 3-month, p=0.0046 at 1-year) difference in percentage of volume change was observed based on leiomyoma location; submucous leiomyomas showed the largest volume reduction. The initial leiomyoma volume showed a weak negative correlation (Spearman's correlation-coefficient =-0.35 at 3m and -0.36 at 1y) with the leiomyoma volume change. For the second part the tube angle prediction resulted in a significant reduction of the radiation dose utilized (p<0.001), fluoroscopy time (p=0.002) and contrast medium volume (p<0.001) for the sample patients when compared with the control patients. The overall radiation dose was reduced from a mean of 11044 μGym2 to a mean of 4172.5 μGym2, fluoroscopy time was reduced from a mean of 15.45 minutes to 8.81 minutes and contrast medium volume was reduced from a mean of 135 ml to 75 ml. Conclusion: UAE results in significant leiomyoma volume reduction at 3-month and 1- year follow-up. The leiomyoma location plays an important role in volume changes while the initial leiomyoma volume plays a minor role. Pre-procedural prediction of the best tube angle obliquity for visualization of the origin of the uterine artery using 3D-reconstructed CE-MRA results in a significant reduction of the radiation dose, fluoroscopy time and contrast medium volume used during UAE.
Post-translational modifications (PTMs) of cell fate regulating proteins determine their stability, localization and function and control the activation of cell protective signaling pathways. Particularly in aberrantly dividing cancer cells the surveillance of cell cycle progression is essential to control tumorigenicity. In a variety of carcinomas, lymphomas and leukemias, the tumor-suppressive functions of the apoptosis- and senescence-regulating promyelocytic leukemia protein (PML) is controlled by numerous PTMs. PML poly-ubiquitylation and polySUMOylation at several lysine (K) residues induce PML degradation that is correlated to a progressive and invasive cancer phenotype. Besides several known E3 ubiquitin protein ligases that are involved in PML degradation, less is known about PML-specific deubiquitylases (DUBs), the respective DUB-controlled ubiquitin conjugation sites and the functional consequences of PML (de)ubiquitylation. Here, we show that the pro-tumorigenic DUB USP22 critically regulates PML protein stability by modifying PML residue K394 in advanced colon carcinoma cells in vitro and that this modification also impacts the homeostasis and function of the leukemia-associated mutant variant PML-RARα. We found that ablation of USP22 decreases PML mono-ubiquitylation and correlates with a prolonged protein half-live in colon carcinoma and acute promyelocytic leukemia (APL) cell lines. Additionally, silencing of USP22 enhances interferon and interferon-stimulated gene (ISG) expression in APL cells in vitro, which together with prolonged PML-RARα stability increases the APL cell sensitivity towards differentiation treatment. In accordance with the novel roles of USP22 as suppressor of the interferon response in human intestinal epithelial cells (hIECs), our findings imply USP22-dependent surveillance of PML-RARα stability and interferon signaling in human leukemia cells, revealing USP22 as central regulator of leukemia pathogenesis.
Using walls to navigate the room: egocentric representations of borders for spatial navigation
(2021)
Spatial navigation forms one of the core components of an animal’s behavioural repertoire. Good navigational skills boost survival by allowing one to avoid predators, to search successfully for food in an unpredictable world, and to be able to find a mating partner. As a consequence, the brain has dedicated many of its resources to the processing of spatial information. Decades of seminal work has revealed how the brain is able to form detailed representations of one’s current position, and use an internal cognitive map of the environment to traverse the local space. However, what is much less understood is how neural computations of position depend on distance information of salient external locations such as landmarks, and how these distal places are encoded in the brain.
The work in this thesis explores the role of one brain region in particular, the retrosplenial cortex (RSC), as a key area to implement distance computations in relation to distal landmarks. Previous research has shown that damage to the RSC results in losses of spatial memory and navigation ability, but its exact role in spatial cognition remains unclear. Initial electrophysiological recordings of single cells in the RSC during free exploration behaviour of the animal resulted in the discovery of a new population of neurons that robustly encode distance information towards nearby walls throughout the environment. Activity of these border cells was characterized by high firing rates near all boundaries of the arena that were available to the animal, and sensory manipulation experiments revealed that this activity persisted in the absence of direct visual or somatosensory detection of the wall.
It quickly became apparent that border cell activity was not only modulated by the distance to walls, but was contingent on the direction the animal was facing relative to the boundary. Approximately 40% of neurons displayed significant selectivity to the direction of walls, mostly in the hemifield contra-lateral to the recorded hemisphere, such that a neuron in left RSC is active whenever a wall occupies proximal space on the right side of the animal. Using a cue-rotation paradigm, experiments initially showed that this egocentric direction information was invariant to the physical rotation of the arena. Yet this rotation elicited a corresponding shift in the preferred direction of local head-direction cells, as well as a rotation in the firing fields of spatially-tuned cells in RSC. As a consequence, position and direction encoding in RSC must be bound together, rotating in unison during the environmental manipulations, as information about allocentric boundary locations is integrated with head-direction signals to form egocentric border representations.
It is known that the RSC forms many anatomical connections with other parts of the brain that encode spatial information, like the hippocampus and para-hippocampal areas. The next step was to establish the circuit mechanisms in place for RSC neurons to generate their activity in respect to the distance and direction of walls. A series of inactivation experiments revealed how RSC activity is inter-dependent with one of its communication partners, the medial entorhinal cortex (MEC). Together they form a wider functional network that encodes precise spatial information of borders, with information flowing from the MEC to RSC but not vice versa. While the conjunction between distance and heading direction relative to the outer walls was the main driver of neural activity in RSC, border cells displayed further behavioural correlates related to movement trajectories. Spiking activity in either hemisphere tended to precede turning behaviour on a short time-scale in a way that border cells in the right RSC anticipated right-way turns ~300 ms into the future.
The interpretation of these results is that the RSC’s primary role in spatial cognition is not necessarily on the early sensory processing stage as suggested by previous studies. Instead, it is involved in computations related to the generation of motion plans, using spatial information that is processed in other brain areas to plan and execute future actions. One potential function of the RSC’s role in this process could be to act correctly in relation to the nearby perimeter, such that border cells in one hemisphere are involved in the encoding of walls in the contralateral hemifield, after which the animal makes an ipsilateral turn to avoid collision. Together this supports the idea that the MEC→RSC pathway links the encoding of space and position in the hippocampal system with the brain’s motor action systems, allowing animals to use walls as prominent landmarks to navigate the room.
Anthropogenic activities have a major impact on our planet and rapidly drive biodiversity loss in ecosystems at a global scale. Particularly over the last century, rising CO2 emissions significantly raised global temperatures and increased the intensity and frequency of droughts and heatwaves. Additionally, agricultural land use and fossil fuel combustion contribute to the continuous release of nitrogen (N) and phosphorus (P) into ecosystems worldwide through extensive fertilization and deposition from the atmosphere. It is important to understand how these rapid changes affect the evolution of plant populations and their adaptive potential. Adaptation by natural selection (i.e., adaptive evolution) within a few generations is an essential process as a response to rapid environmental changes. Rapid evolution of plant populations can be detected by using the so-called resurrection approach. Here, diaspores (i.e., seeds) from a population are collected before (ancestors) and after (descendants) a potential selection pressure (e.g., consecutive years of drought or changes in nutrient supply). Comparing phenotypes of ancestors and descendants in a common environment such as an outside garden, greenhouse, or climate chamber, may then reveal evolutionary changes. Ideally, plants are first grown in a common environment for an intermediate refresher generation to reduce parental and storage effects.
The aim of this thesis was to investigate the occurrence of adaptive evolution in natural plant populations in response to rapidly changing environments over the past three decades. I conducted three experiments using the resurrection approach to generate comprehensive data on the adaptive processes that acted on three plant populations from three different species over the last three decades. Furthermore, I filled knowledge gaps in plant evolutionary ecology and conceptually developed the resurrection approach further.
In Chapter I, I performed a novel approach by testing for adaptive evolution in natural plant populations using the resurrection approach in combination with in-situ transplantations. I cultivated seedlings from ancestors (23 – 26 years old) and contemporary descendants of three perennial species (Melica ciliata, Leontodon hispidus and Clinopodium vulgare) from calcareous grasslands in the greenhouse and In Chapter III, I assessed the reproducibility of phenotypic differences between genotypes among three different growth facilities (climate chamber, greenhouse, and outdoor garden). I also evaluated differences in phenotypic expression between plants grown after one vs. two intermediate generations (i.e., refresher generations). I performed this experiment within the framework of the resurrection approach and compared ancestors and descendants of the same population of Leontodon hispidus.
I observed very strong differences among plants growing in the different growth facilities. I found a significant interaction between the growth facility and the temporal origin (ancestors vs. descendants): descendants had significantly larger rosettes than ancestors only in the greenhouse and they flowered significantly later than ancestors exclusively in the climate chamber. I did not find significant differences between intermediate generations within the growth facilities. Overall, Chapter III shows that the use of a particular experimental system can dictate the presence and magnitude of phenotypic differences. This implies that absence of evidence is not evidence of absence when it comes to investigating genetically based trait differentiation among plant origins (in space or time). Experimental systems should be carefully designed to provide meaningful conditions, ideally mimicking the environmental conditions of the population’s origins. Finally, growing a second intermediate generation did not impact the genetic differences of ancestors and descendants within the environments, supporting the idea that only one intermediate generation may be sufficient to reduce detectable parental and storage effects.
The resurrection approach allows a better understanding of rapid plant adaptation, but some limitations deserve to be highlighted. I only studied one population per species, and Chapters II and III only focus on one population of L. hispidus, which is also hampering generalizations, as adaptive potential can vary greatly among populations of the same species. I only compared the ancestral genotypes to one descendant sample with a long time span in between (26 – 28 years), which makes it hard to pinpoint the selection agents that caused the genetic differentiation among the sampling years. Hence, closely monitoring biotic and abiotic factors of the studied populations between the ancestral and descendant sampling in future studies, would make identifying the responsible selection pressures more precise. I also recommend sampling multiple populations over consecutive years to improve the robustness of results and make generalizations more approachable.Furthermore, combining the resurrection approach with other methods such as in-situ transplantations will be valuable to offset the limitation that adaptations cannot be proven under artificial conditions (e.g., in the greenhouse).
Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP to dihydroneopterin triphosphate (H2NTP), the initiating step in the biosynthesis of tetrahydrobiopterin (BH4). Besides other roles, BH4 functions as cofactor in neurotransmitter biosynthesis. The BH4 biosynthetic pathway and GCH1 have been identified as promising targets to treat pain disorders in patients. The function of mammalian GCH1s is regulated by a metabolic sensing mechanism involving a regulator protein, GCH1 feedback regulatory protein (GFRP). GFRP binds to GCH1 to form inhibited or activated complexes dependent on availability of cofactor ligands, BH4 and phenylalanine, respectively. We determined high-resolution structures of human GCH1−GFRP complexes by cryoelectron microscopy (cryo-EM). Cryo-EM revealed structural flexibility of specific and relevant surface lining loops, which previously was not detected by X-ray crystallography due to crystal packing effects. Further, we studied allosteric regulation of isolated GCH1 by X-ray crystallography. Using the combined structural information, we are able to obtain a comprehensive picture of the mechanism of allosteric regulation. Local rearrangements in the allosteric pocket upon BH4 binding result in drastic changes in the quaternary structure of the enzyme, leading to a more compact, tense form of the inhibited protein, and translocate to the active site, leading to an open, more flexible structure of its surroundings. Inhibition of the enzymatic activity is not a result of hindrance of substrate binding, but rather a consequence of accelerated substrate binding kinetics as shown by saturation transfer difference NMR (STD-NMR) and site-directed mutagenesis. We propose a dissociation rate controlled mechanism of allosteric, noncompetitive inhibition.
The aim of this work was to establish a new way of predicting novel dual active compounds by combining classical fingerprint representation with state-of-the-art machine learning algorithms. Advantages and disadvantages of the applied 2D- and 3D-fingerprints were investigated. Further, the impact of various machine learning algorithms was analyzed. The new method developed in this work was used to predict compounds, which inhibit two different targets (LTA4H and sEH) involved in the same disease pattern (inflammation). The development of multitarget drugs has become more important in recent years. Many widespread diseases like metabolic syndrome, or cancer are of a multifactorial nature, which makes them hard to be treated effectively with a single drug. The new in silico method presented in this work can help to accelerate the design and development of multitarget drugs, saving time and efforts.
The nowadays readily available access to a large number of 3D-structures of biological targets and published activity data of millions of synthesized compounds enabled this study and was used as a starting point for this work. Four different data sets were compiled (crystalized ligands from the PDB, active and inactive compounds from ChEMBL23, newly designed compounds using a combinatorial library). Those data sets were collected and processed using an automated KNIME workflow. This automation has the advantage of allowing easy change and update of compound sources and adapted processing ways.
In a next step, the compounds from the compiled data sets were represented using a variety of well-established 2D- and 3D-fingerprints (PLIF, AtomPair, Morgan, FeatMorgan, MACCS). All those fingerprints share the same underlying bit string scheme but vary in the way they describe the molecular structure. Especially the difference between 2D- and 3D-fingerprints was investigated. 2D-fingerprints are solely based on ligand information. 3D-fingerprints, on the other hand, are based on X-ray structure information of protein-ligand complexes. One major difference between 2D- and 3D-fingerprints usage is the need for a 3D-conformation (pose) of the compound in the targets of interest when using 3D-fingerprints. This additional step is time-consuming and brings further uncertainties to the method.
Based on the calculated fingerprints state-of-the-art machine learning algorithms (SVC, RF, XGB and ADA) were used to predict novel dual active compounds. The models were evaluated by 10-fold cross validation and accuracy as the primary measure of model performance was maximized. Second, individual parameters of the four machine learning algorithms were optimized in a grid search to achieve maximal accuracy using the optimized partitioning scheme. Overall accuracies, regardless of fingerprint and machine learning algorithm, are slightly better for LTA4H than for sEH.
The goal to predict dual active compounds was realized by comparing the set of predicted to be active compounds for LTA4H and sEH. For the 3D-fingerprint PLIF the machine learning algorithm Random Forest was chosen, from which compounds for synthesis and testing were selected. Of 115 predicted to be active compounds, six compounds were cherry picked. Two compounds showed very good/moderate dual inhibitory activity. Of the 2D-fingerprints, the AtomPair fingerprint in combination with the machine learning algorithm Random Forest was chosen from which compounds were selected for synthesis and testing. 116 compounds were predicted to be dual active against LTA4H and sEH. One of those compounds showed good dual inhibitory activity.
In this work it was possible to show advantages and disadvantages of using 2D- and 3D-fingerprints in combination with machine learning algorithms. Both strategies (2D: ligand-based, 3D: structure-based) lead to the prediction of novel dual active compounds with moderate to very good inhibitory activity. The method developed in this work is able to predict dual active compounds with very good inhibitory activity and novel (previously unknown) scaffolds inhibiting the targets LTA4H and sEH. This contribution to in silico drug design is promising and can be used for the prediction of novel dual active compounds. Those compounds can further be optimized regarding binding affinity, solubility and further pharmacological and physicochemical properties.
This thesis combines behavioral and cognitive approaches regarding the Web for analyzing users' behavior and supposed interests.
The work is placed in a new field of research called Web Science, which includes, but is not restricted to, the analysis of the World Wide Web. The term Web Science is affected by Tim Berners-Lee et al., who invited the researchers to "create a science of the web" [BLHH+06a]. The thesis is structured in two parts, reflecting the intersection of disciplines that is required for Web Science.
The first part is related to computer science and information systems. This part defines the Gugubarra concepts and algorithms for web user profiling and builds upon the results by Mushtaq et al. [MWTZ04]. This profiling aims at understanding the behavior and supposed interests of users. Based on these concepts, a framework was implemented to support the needs of web site owners. The core technologies used are Java, Spring, Hibernate, and content management systems. The design principles, architecture, implementation, and tests of the prototype are reported.
The second part is directly related to behavioral economics and is connected to the areas of economics, mathematics, and psychology. This part contributes to behavior models, as was claimed by Tim Berners-Lee et al.: "Though individual users may or may not be rational, it has long been noted that en masse people behave as utility maximisers. In that case, understanding the incentives that are available to web users should provide methods for generating models of behaviour..."[BLHH+06b]. The focus here is on studies that investigate the user's choice of online information services in a multi-attribute context. The introduced research framework takes into account background and local context effects and builds upon theoretical foundations by Tversky and Kahneman [TK86]. The findings provide useful insights to behavioral scientists and to practitioners on how to use framing strategies to alter the user's choice.
Mitogen activated protein kinases (MAPKs) are found in all eukaryotic cells and represent crucial elements in the signal transduction from the plasma membrane to the nucleus. Although a broad variety of extracellular stimuli activate MAPKs, they evoke very distinct cellular responses. The amplitude and duration of MAPK activation determine signal identity and ultimately cell fate. A tight and finely tuned regulation is therefore critical for a specific cellular response. The role and the regulation of extracellular signal-regulated kinase 5 (ERK5), a MAPK with a large and unique C-terminal tail, were studied in different cellular systems. The study highlights two aspects of ERK5 regulation: control of the phosphorylation state and regulated protein stability. In analogy to other MAPKs ERK5 is activated by dual phosphorylation of threonine and tyrosine residues in its activation motif. A first part of the study concentrates on whether and how the protein tyrosine phosphatase PTP-SL is involved in the downregulation of the ERK5 signal. The direct interaction of both proteins is shown to result in mutual modulation of their enzymatic activities. PTP-SL is a substrate of ERK5 and, independent of its phosphorylation, binding to the kinase enhances its catalytic phosphatase activity. On the other hand, interaction with PTP-SL does not only downregulate enzymatic ERK5 activity but also effectively impedes its translocation to the nucleus. The second part of this study focuses on the interaction of ERK5 with c-Abl and its oncogenic variants Bcr/Abl and v-Abl. In this study these tyrosine kinases are demonstrated to regulate ERK5 by two mechanisms: first, by induction of kinase activity and secondly, by stabilisation of the ERK5 protein. Stabilisation involves the direct interaction of unique ERK5 domains with Abl kinases and is independent of MAPK cascade activation. The level of ERK5 and its intrinsic basal activity – rather than its activation – are essential for v-Abl-induced transformation as well as for survival of Bcr/Abl-positive leukaemia cells. Stabilisation of ERK5 thus contributes to cell survival and should therefore be considered as an additional aspect in therapy of chronic myeloid leukaemia. Taken together, the results obtained in this study demonstrate that diverse pathways regulate ERK5 signalling by affecting kinase activity, localisation and protein stability. While the phosphatase PTP-SL is involved in negative regulation of ERK5, Abl kinases potently activate ERK5 and increase its half-life. Protein stabilisation thus is presented as a novel mechanism in the regulation of MAPKs.
The thesis entitled „Investigations on the significance of nucleo-cytoplasmic transport for the biological function of cellular proteins" aimed to unreveal molecular mechanisms in order to improve our understanding of the impact of nucleo-cytoplasmic transport on cellular functions. Within the scope of this work, it could be shown that regulated nucleo-cytoplasmic transport of a subfamily of homeobox transcription factors controlled their intra- and intercellular transport, and thereby influencing also their transcriptional activity. This study describes a novel regulatory mechanism, which could in general play an important role for the ordered differentiation of complex organisms. Besides cis-active transport Signals, also post-translational modifications can influence the localization and biological activity of proteins in trans. In addition to the known impact of phosphorylation on the transport and activity of STAT1, experimental evidence was provided demonstrating that acetylation affected the interaction of STAT1 with NF-kB p65, and subsequently modulated the expression of apoptosis-inducing NF-kB target genes. The impact of nucleo-cytoplasmic transport on the regulation of apoptosis was underlined by showing that the evolutionary conservation of a NES within the anti-apoptotic protein survivin plays an essential role for its dual function in the inhibition of apoptosis and ordered cell division. Since survivin is considered a bona fide cancer therapy target, these results strongly encourage future work to identify molecular decoys that specifically inhibit the nuclear export of survivin as novel therapeutics. In order to further dissect the regulation of nuclear transport and to efficiently identify transport inhibitors, cell-based assays are urgently required. Therefore, the cellular assay Systems developed in this work may not only serve to identify synthetic nuclear export and Import inhibitors but may also be applied in systematic RNAi-screening approaches to identify novel components of the transport machinery. In addition, the translocation based protease- and protein-interaction biosensors can be applied in various biological Systems, in particular to identify protein-protein interaction inhibitors of cancer relevant proteins. In summary, this work does not only underline the general significance of nucleo-cytoplasmic transport for cell biology, but also demonstrates its potential for the development of novel therapies against diseases like cancer and viral infections.
This thesis contributes to the field of machine learning with a specific focus on the methods for learning relations between the inputs. Learning relationships between images is the most common primitive in vision. There are many vision tasks in which relationships across images play an important role. Some of them are motion estimation, activity recognition, stereo vision, multi-view geometry and visual odometry. Many of such tasks mainly depend on motion and disparity cues, which are inferred based on the relations across multiple image pairs. The approaches presented in this thesis mainly deal with, but are not limited to, learning of the representations for motion and depth. This thesis by articles consists of five articles which present relational feature learning models along with their applications in computer vision. In the first article, we present an approach for encoding motion in videos. To this end, we show that the detection of spatial transformations can be viewed as detection of coincidence or synchrony between the given sequence of frames and a sequence of features which are related by the transformation we wish to detect. Learning to detect synchrony is possible by introducing "multiplicative interactions'' into the hidden units of single layered sparse coding models.
We show that the learned motion representations employed for the task of activity recognition achieve competitive performance on multiple benchmarks. Stereo vision is an important challenge in computer vision and useful for many applications in that field. In the second article, we extend the energy based learning models, which were previously used for motion encoding, to the context of depth perception. Given the common architecture of the models for encoding motion and depth, we show that it is possible to define a single model for learning a unified representation for both the cues. Our experimental results show that learning a combined representation for depth and motion makes it possible to achieve state-of-the-art performance at the task of 3-D activity analysis, and to perform better than the existing hand-engineered 3-D motion features. Autoencoder is a popular unsupervised learning method for learning efficient encoding for a given set of data samples. Typically, regularized autoencoders which are used to learn over-complete and sparse representations for the input data, were shown to fail on intrinsically high dimensional data like videos. In the third article, we investigate the reason for such a behavior. It can be observed that the regularized autoencoders typically learn negative hidden unit biases. We show that the learning of negative biases is the result of hidden units being responsible for both the sparsity and the representation of the input data. It is shown that, as a result, the behavior of the model resembles clustering methods which would require exponentially large number of features to model intrinsically high dimensional data. Based on this understanding, we propose a new activation function which decouples the roles of hidden layer and uses linear encoding. This allows to learn representations on data with very high intrinsic dimensionality. We also show that gating connections in the bi-linear models and the single layer models from articles one and two of this thesis can be thought of as a way to attain a linear encoding scheme which allows them to learn good representations on videos. Visual odometry is the task of inferring egomotion of a moving object from visual information such as images and videos. It can primarily be used for the task of localization and has many applications in the fields of robotics and navigation. The work in article four was motivated by the idea of using deep learning techniques, which are successful methods for many vision tasks, for visual odometry. The visual odometry task mainly requires inference of motion and depth information from visual input which can then be mapped to velocity and change in direction. We use relational feature models presented in the articles one and two for inferring a combined motion and depth representation from stereo video sequences. The combined representation is then mapped to discrete velocity and change in direction labels using convolutional neural networks. Our approach is an end-to-end deep learning-based architecture which uses a single type of computational model and learning rule. Preliminary results show that the architecture is capable of learning the mapping from input video to egomotion. Activity recognition is a challenging computer vision task with many real world applications. It is well know that it is a hard task to use computer vision research for real-time applications. In the fifth article of this thesis, we present a real-time activity recognition system based on deep learning based methods. Our approach uses energy based relational feature learning models for the computation of local motion features directly from videos. A bag-of-words over the local motion features is used for the analysis of activity in a given video sequence. We implement this system on a distributed computational platform and demonstrate its performance on the iCub robot. Using GPUs we demonstrate real time performance which makes the deployment of activity recognition systems in real world scenarios possible.
Geochemical investigations on biogenic carbonates are commonly conducted to reconstruct the environmental conditions of the past. However, different carbonate producers incorporate elements to varying degrees, due to biological vital effects. Detecting and quantifying these effects is crucial to produce reliable reconstructions. These paleoreconstructions are of great importance to evaluate the consequences of our recent climate change and identify control mechanisms on the distribution of endangered species such as Desmophyllum pertusum. In chapter three we tested Mg/Ca, Sr/Ca and Na/Ca ratios on this species, among other coldwater scleractinians, to test if they provide reliable proxy information. The results reveal no apparent control of Mg/Ca or Sr/Ca ratios through seawater temperature, salinity or pH. Na/Ca ratios appear to be partly controlled by the seawater temperature, which is also true for other aragonitic organisms such as warm-water corals and the bivalve Mytilus edulis. However, a large variability complicates possible reconstructions by means of Na/Ca. In addition, we explore different models to explain the apparent temperature effect on Na/Ca ratios based on temperature sensitive Na and Ca pumping enzymes.
The bivalve Acesta excavata is commonly found in cold-water coral reefs among the North Atlantic, together with D. pertusum. Multiple linear regression analysis, presented in chapter four, indicates that up to 79% of the elemental variability in Mg/Ca, Sr/Ca and Na/Ca is explainable with temperature and salinity as independent predictor variables. Vital effects, for instance growth rate effects, are evident and make paleoreconstructions not feasible. Furthermore, organic material embedded in the shell, as well as possible stress effects can drastically change the elemental composition. Removal of these organic matrices from bulk samples for LA-ICP-MS (laser ablation inductively coupled mass spectrometer) measurements by means of oxidative cleaning is not possible, but Na/Ca ratios decrease after this cleaning. This is presumably an effect of leaching and not caused by the removal of organic matrices.
Interesting biogeochemical relations were found in the parasitic foraminifera H. sarcophaga. We report Mg/Ca, Sr/Ca, Na/Ca and Mn/Ca ratios measured in H. sarcophaga from two different host species (A. excavata and D. pertusum) in chapter five. Sr/Ca ratios are significantly higher in foraminifera that lived on D. pertusum. This could indicate that dissolved host material is utilized in shell calcification of H. sarcophaga, given the naturally higher strontium concentration in the aragonite of D. pertusum. Mn/Ca ratios are highest in foraminifera that lived on A. excavata but did not fully penetrate the host’s shell. Most likely, this represents a juvenile stadium of the foraminifera during which it feeds on the organic
periostracum of the bivalve, which is enriched in Mn and Fe. The isotopic compositions are similarly affected, both δ18O and δ13C values are significantly lower in foraminifera that lived 23on D. pertusum compared to specimen that lived on A. excavata. Again, this might represent the uptake of dissolved host material or different pH regimes in the calcifying fluid of the hosts (bivalve < 8, coral > 8) that control the extent of hydration/hydroxylation reactions. Temperature reconstructions are possible using stable oxygen isotopes on this foraminifera species; however, the results are only reliable if the foraminifera lived on A. excavata. Samples of H. sarcophaga from D. pertusum would lead to overestimations of the seawater temperature due to the lower δ18O values.
Apart from biological vital effects, storage and preservation methods can significantly change the geochemical composition of different marine biogenic carbonates. In chapter six this is presented on the example of ethanol preservation, a common technique to allow extended storage of biogenic samples. The investigation reveals a significant decrease of Mg/Ca and Na/Ca ratios even after only 45 days storage in ultrapure ethanol. Sr/Ca ratios on the other hand are not influenced.
Besides temperature, salinity and pH further environmental parameters are important such as nutrient availability, especially for the distribution of cold-water corals. In chapter seven we extend the investigations on A. excavata by including the elemental ratios Ba/Ca, Mn/Ca and P/Ca. We expected P/Ca to be helpful in the otherwise difficult process of dentifying growth increments. Based on our observations we had to refute this theory. P/Ca ratios are not systematically enriched in the vicinity of growth lines. Instead, we found a regular sequence of peaks of Ba/Ca, P/Ca and Mn/Ca. This sequence as well as the peaks in general are potentially caused by equential blooms of different algae, diatoms and other planktonic organisms ...
Ubiquitination is regarded as one of the key post-translational modifications in nearly all biological processes, endowed with numerous layers of complexity. Deubiquitinating enzymes (DUBs) dynamically counterbalance ubiquitination events by deconjugating ubiquitin signals from substrates. Dysregulation of the ubiquitin code and its negative regulators drive various pathologies, such as neurological disorders and cancer.
The DUB ubiquitin-specific peptidase 22 (USP22) is well-known for its essential role in the human Spt-Ada-Gcn5 acetyltransferase (SAGA) complex, mediating the removal of monoubiquitination events from Histone 2A and 2B (H2A and -B), thereby regulating gene transcription. In cancer, USP22 was initially described as a part of an 11-gene expression signature profile, predicting tumor metastasis, reoccurrence and death after therapy in a wide range of tumor cells. However, novel roles for USP22 have emerged recently, accrediting USP22 essential roles in regulating tumor development as well as apoptotic cell death signaling.
One of the hallmarks of cancer is the evasion of cell death, especially apoptosis, a form of programmed cell death (PCD). Necroptosis, a regulated form of necrosis, is regarded as an attractive therapeutic strategy to overcome apoptosis-resistance in tumor cells, although a profound understanding of the exact signaling cascade still remains elusive. Nevertheless, several ubiquitination and deubiquitination events are described in fine-tuning necroptotic signaling.
In this study, we describe a novel role for USP22 in regulating necroptotic cell death signaling in human tumor cell lines. USP22 depletion significantly delayed TNFa/Smac mimetic/zVAD.fmk (TBZ)-induced necroptosis, without affecting TNFa-induced nuclear factor-kappa B (NF-KB) signaling or TNFa-mediated extrinsic apoptosis. Intriguingly, re-expression of USP22 wildtype in the USP22 knockout background could re-sensitize HT-29 cells to TBZ-induced necroptosis, whereas re-constitution with the catalytic inactive mutant USP22 Cys185Ser did not rescue susceptibility to TBZ-induced necroptosis, confirming the USP22 DUB-function a pivotal role in regulating necroptotic cell death. USP22 depletion facilitated ubiquitination and unexpectedly also phosphorylation of Receptor-interacting protein kinase 3 (RIPK3) during necroptosis induction, as shown by Tandem Ubiquitin Binding Entities (TUBE) pulldowns and in vivo (de)ubiquitination immunoprecipitations. To substantiate our findings, we performed mass-spectrometric ubiquitin remnant profiling and identified the three novel USP22-regulated RIPK3 ubiquitination sites Lysine (K) 42, K351 and K518 upon TBZ-induced necroptosis. Further assessment of these ubiquitination sites unraveled, that mutation of K518 in RIPK3 reduced necroptosis-associated RIPK3 ubiquitination and additionally affected RIPK3 phosphorylation upon necroptosis induction. At the same time, genetic knock-in of RIPK3 K518R sensitizes tumor cells to TNFa-induced necroptotic cell death and amplified necrosome formation.
In summary we identified USP22 as a new regulator of TBZ-induced necroptosis in various human tumor cell lines and further unraveled the distinctive role of DUBs and (de)ubiquitination events in controlling programmed cell death signaling.
Ultrafast protein dynamics are of great interest for understanding the molecular basis of biochemical function. One method to study structural changes with highest time-resolution starting in the femtosecond regime is 2D-IR spectroscopy. However its application to investigate protein dynamics both with high temporal and spatial resolution is currently limited to few biological systems with intrinsic chromophores. Spectral congestion, the contribution of many similar oscillators to the same signals, makes it difficult to draw conclusions about local structural dynamics in most other proteins.
The aim of this thesis is to extend the application of 2D-IR spectroscopy to a wider range of proteins by introducing unnatural amino acids (UAAs) with azide or nitrile groups as site-specific vibrational probes, which absorb in the free spectral window between 1800 to 3000 cm-1 by using methods from chemical biology.
In a comparative experimental study using FTIR and 2D-IR spectroscopy of single amino acids azidohomoalanine (Aha), a methionine analogue, was identified as preferred label. To demonstrate the application potential of UAAs as site-specific probes, Aha was then incorporated into different positions in a small globular protein. By using both FTIR and ultrafast 2D-IR it was shown, that indeed the local microenvironment as well as conformational fluctuations on picosecond timescale could be monitored with high spatial information. The azide moiety shows a shift of its absorption frequency depending on the polarity of its surrounding. Using this approach, different subensembles for the protein conformations with more polar and less polar environment around the vibrational probe can be distinguished.
A second major application of site-specific labels is the study of vibrational energy transfer processes (VET), predicted to be relevant for allosteric communication in protein domains such as the PDZ domain. VET can be tracked with high spatial resolution using time-resolved IR spectroscopy by exciting a localized vibrational mode and probing separate modes in a two-colour 2D-IR experiment. To extend this kind of experiment to proteins, a specific donor-acceptor pair of two UAAs was introduced. It uses an azulene moiety as donor that can be excited in the visible range but deposits the excess energy by internal conversion into the vibrational modes of the ground state. In small peptides this VET pair was applied successfully, showing a distance-dependent energy transfer induced signal for VET through covalent bonds. These findings bare great promise for the direct observation of vibrational energy flow in proteins in real-time.
Overall this thesis is the basis for extending the usability of 2D-IR spectroscopy to study structural dynamics in a wide range of proteins systems both with high temporal and spatial resolution.
Die Emergenz digitaler Netzwerke ist auf die ständige Entwicklung und Transformation neuer Informationstechnologien zurückzuführen.
Dieser Strukturwandel führt zu äußerst komplexen Systemen in vielen verschiedenen Lebensbereichen.
Es besteht daher verstärkt die Notwendigkeit, die zugrunde liegenden wesentlichen Eigenschaften von realen Netzwerken zu untersuchen und zu verstehen.
In diesem Zusammenhang wird die Netzwerkanalyse als Mittel für die Untersuchung von Netzwerken herangezogen und stellt beobachtete Strukturen mithilfe mathematischer Modelle dar.
Hierbei, werden in der Regel parametrisierbare Zufallsgraphen verwendet, um eine systematische experimentelle Evaluation von Algorithmen und Datenstrukturen zu ermöglichen.
Angesichts der zunehmenden Menge an Informationen, sind viele Aspekte der Netzwerkanalyse datengesteuert und zur Interpretation auf effiziente Algorithmen angewiesen.
Algorithmische Lösungen müssen daher sowohl die strukturellen Eigenschaften der Eingabe als auch die Besonderheiten der zugrunde liegenden Maschinen, die sie ausführen, sorgfältig berücksichtigen.
Die Generierung und Analyse massiver Netzwerke ist dementsprechend eine anspruchsvolle Aufgabe für sich.
Die vorliegende Arbeit bietet daher algorithmische Lösungen für die Generierung und Analyse massiver Graphen.
Zu diesem Zweck entwickeln wir Algorithmen für das Generieren von Graphen mit vorgegebenen Knotengraden, die Berechnung von Zusammenhangskomponenten massiver Graphen und zertifizierende Grapherkennung für Instanzen, die die Größe des Hauptspeichers überschreiten.
Unsere Algorithmen und Implementierungen sind praktisch effizient für verschiedene Maschinenmodelle und bieten sequentielle, Shared-Memory parallele und/oder I/O-effiziente Lösungen.
Vibronic (vibrational-electronic) transition is one of the fundamental processes in molecular physics. Indeed, vibronic transition is essential both in radiative and nonradiative photophysical or photochemical properties of molecules such as absorption, emission, Raman scattering, circular dichroism, electron transfer, internal conversion, etc. A detailed understanding of these transitions in varying systems, especially for (large) biomolecules, is thus of particular interest. Describing vibronic transitions in polyatomic systems with hundreds of atoms is, however, a difficult task due to the large number of coupled degrees of freedom. Even within the relatively crude harmonic approximation, such as for Born-Oppenheimer harmonic potential energy surfaces, the brute-force evaluation of Franck-Condon intensity profiles in a time-independent sum-over-states approach is prohibitive for complex systems owing to the vast number of multi-dimensional Franck-Condon integrals. The main goal of this thesis is to describe a variety of molecular vibronic transitions, with special focus on the development of approaches that are applicable to extended molecular systems. We use various representations of Fermi’s golden rule in frequency, time and phase spaces via coherent states to reduce the computational complexity. Although each representation has benefits and shortcomings in its evaluation, they complement each other. Peak assignment of a spectrum can be made directly after calculation in the frequency domain but this sum-over-states route is usually slow. In contrast, computation is considerably faster in the time domain with Fourier transformation but the peak assignment is not directly available. The representation in phase space does not immediately provide physically-meaningful quantities but it can link frequency and time domains. This has been applied to, herein, for example (non-Condon) absorption spectra of benzene and electron transfer of bacteriochlorophyll in the photosynthetic reaction center at finite temperature. This work is a significant step in the treatment of vibronic structure, allowing for the accurate and efficient treatment of complex systems, and provides a new analysis tool for molecular science.
Topological phases set themselves apart from other phases since they cannot be understood in terms of the usual Landau theory of phase transitions. This fact, which is a consequence of the property that topological phase transitions can occur without breaking symmetries, is reflected in the complicated form of topological order parameters. While the mathematical classification of phases through homotopy theory is known, an intuition for the relation between phase transitions and changes to the physical system is largely inhibited by the general complexity.
In this thesis we aim to get back some of this intuition by studying the properties of the Chern number (a topological order parameter) in two scenarios. First, we investigate the effect of electronic correlations on topological phases in the Green's function formalism. By developing a statistical method that averages over all possible solutions of the manybody problem, we extract general statements about the shape of the phase diagram and investigate the stability of topological phases with respect to interactions. In addition, we find that in many topological models the local approximation, which is part of many standard methods for solving the manybody lattice model, is able to produce qualitatively correct phase transitions at low to intermediate correlations.
We then extend the statistical method to study the effect of the lattice, where we evaluate possible applications of standard machine learning techniques against our information theoretical approach. We define a measure for the information about particular topological phases encoded in individual lattice parameters, which allows us to construct a qualitative phase diagram that gives a more intuitive understanding of the topological phase.
Finally, we discuss possible applications of our method that could facilitate the discovery of new materials with topological properties.
The compound class of the fabclavines was described as secondary or specialized metabolites (SM) for Xenorhabdus budapestensis and X. szentirmaii. Their corresponding structure was elucidated by NMR and further derivatives could be identified in both strains. Biochemically, fabclavines are hybrid SMs derived from two non-ribosomal-peptide-synthetases (NRPS), one type I polyketide-synthase (PKS) and polyunsaturated fatty acid (PUFA) synthases. In detail, a hexapeptide is connected via partially reduced polyketide units to an unsual polyamine. Structurally, they are related to the (pre-)zeamines, described for Serratia plymuthica and Dickeya zeae. Fabclavines exhibit a broad-spectrum bioactivity against a variety of different organisms like Grampositive and Gram-negative bacteria, fungi, protozoa but also against eukaryotic celllines.
In this work, the fabclavine biosynthesis was elucidated and assigned to two independently working assembly lines. The NRPS-PKS-pathway is initiated by the first NRPS FclI via generation of a tetrapeptide, which is elongated by the second NRPS FclJ, leading to a hexapeptide. Alternatively, FclJ can also act as direct start of the biosynthesis, resulting in the final formation of shortened fabclavine derivatives with a diinstead of a hexapeptide. In both cases, the peptide moiety is transferred to the iterative type I PKS FclK, leading to an elongation with partially reduced polyketide units. The resulting NRPS-PKS-intermediate is still enzyme-bound. The PUFA-homologues FclC, FclD and FclE in combination with FclF, FclG and FclH belong to the polyamine-forming pathway. Briefly, repeating decarboxylative Claisen thioester condensation reactions of acyl-coenzym A building blocks lead to the generation of an acyl chain in a PKS- or fatty acid biosynthesis-like manner. The corresponding β-keto-groups are either completely reduced or transaminated in a specific and repetitive way, resulting in the concatenation of so-called amine-units. The final β-keto-group is reduced to a hydroxy-group and the intermediate is reductively released by the thioester reductase FclG. A subsequent transamination step leads to the final polyamine. The NRPS-PKS- as well as the polyamine-pathway are connected by FclL. This condensation domain-like protein catalyzes the condensation of the polyamine with the NRPS-PKS-part, which results in the release of the final fabclavine. The results are described in detail in the first publication (first author).
Fabclavine biosynthesis gene cluster (BGC) are widely spread among the genus Xenorhabdus and Photorhabdus. In Xenorhabdus strains a high degree of conservation regarding the BGC synteny as well as the identity of single proteins can be observed. However, Photorhabdus strains harbor only the PUFA-homologues. While in Photorhabdus no product could be detected, our analysis revealed that the Xenorhabdus strains produce a large chemical diversity of different derivatives. Briefly, the general backbone of the fabclavines is conserved and only four chemical moieties are variable: The second and last amino acids of the NRPS-part, the number of incorporated polyketide units as well as the number of amine units in the polyamine. In combination with the elucidated biosynthesis, these variables could be assigned to single biosynthesis components as diversity mechanisms. Together with the 10 already described derivatives, a total of 32 derivatives could be detected. Interestingly, except for taxonomic closely related strains, all analyzed strains produce their own set of derivatives. Finally, we could confirm that the fabclavines are the major bioactive compound class in the analyzed strains under laboratory conditions. The results are described in detail in the second publication (first author).
Together with our collaboration partner Prof. Selcuk Hazir a potent bioactivity against Enterococcus faecalis, which is associated with endodontic infections, could be contributed to X. cabanillasii. Here, we could confirm that this bioactivity can be assigned to the fabclavines. The results are described in detail in the third publication(co-author).
Among the genus Xenorhabdus, X. bovienii represents an exception as its NRPS and PKS genes of the fabclavine BGC are missing or truncated, resulting in the exclusive production of polyamines. Furthermore, its PUFA-homologue FclC harbors an additional dehydratase (DH) domain. Upon extensive analysis a yet unknown deoxy-polyamine was identified and assigned to this additional domain. Finally, the DH domain was transferred into other polyamine pathways. Regardless of an in cis or in trans integration, the chimeric pathways produced deoxy-derivatives of its naturally occurring polyamines, suggesting that this represents another diversification mechanism. The results are described in detail in the attached manuscript (first author).
Proteins are biological macromolecules playing essential roles in all living organisms.
Proteins often bind with each other forming complexes to fulfill their function. Such protein complexes assemble along an ordered pathway. An assembled protein complex can often be divided into structural and functional modules. Knowing the order of assembly and the modules of a protein complex is important to understand biological processes and treat diseases related to misassembly.
Typical structures of the Protein Data Bank (PDB) contain two to three subunits and a few thousand atoms. Recent developments have led to large protein complexes being resolved. The increasing number and size of the protein complexes demand for computational assistance for the visualization and analysis. One such large protein complex is respiratory complex I accounting for 45 subunits in Homo sapiens.
Complex I is a well understood protein complex that served as case study to validate our methods.
Our aim was to analyze time-resolved Molecular Dynamics (MD) simulation data, identify modules of a protein complex and generate hypotheses for the assembly pathway of a protein complex. For that purpose, we abstracted the topology of protein complexes to Complex Graphs of the Protein Topology Graph Library (PTGL). The subunits are represented as vertices, and spatial contacts as edges. The edges are weighted with the number of contacts based on a distance threshold. This allowed us to apply graph-theoretic methods to visualize and analyze protein complexes.
We extended the implementations of two methods to achieve a computation of Complex Graphs in feasible runtimes. The first method skipped checks for contacts using the information which residues are sequential neighbors. We extended the method to protein complexes and structures containing ligands. The second method introduced spheres encompassing all atoms of a subunit and skipped the check for contacts if the corresponding spheres do not overlap. Both methods combined allowed skipping up to 93 % of the checks for contacts for sample complexes of 40 subunits compared to up to 10 % of the previous implementation. We showed that the runtime of the combined method scaled linearly with the number of atoms compared to a non-linear scaling of the previous implementation We implemented a third method fixing the assignment of an orientation to secondary structure elements. We placed a three-dimensional vector in each secondary structure element and computed the angle between secondary structure elements to assign an orientation. This method sped up the runtime especially for large structures, such as the capsid of human immunodeficiency virus, for which the runtime decreased from 43 to less than 9 hours.
The feasible runtimes allowed us to investigate two data sets of MD trajectories of respiratory complex I of Thermus thermophilus that we received. The data sets differ only by whether ubiquinone is bound to the complex. We implemented a pipeline, PTGLdynamics, to compute the contacts and Complex Graphs for all time steps of the trajectories. We investigated different methods to track changes of contacts during the simulation and created a heat map put onto the three-dimensional structure visualizing the changes. We also created line plots to visualize the changes of contacts over the course of the simulation. Both visualizations helped spotting outstandingly flexible or rigid regions of the structure or time points of the simulation in which major dynamics occur.
We introduced normalizations of the edge weights of Complex Graphs for identi-fying modules and predicting the assembly pathway. The idea is to normalize the number of contacts for the number of residues of a subunit. We defined five different normalizations.
To identify structural and functional modules, we applied the Leiden graph clustering algorithm to the Complex Graphs of respiratory complex I and the respiratory supercomplex. We examined the results for the different normalizations of the weights of the Complex Graphs. The absolute edge weight produced the best result identifying three of four modules that have been defined in the literature for respiratory complex I.
We applied agglomerative hierarchical clustering to the edges of a Complex Graph to create hypotheses of the assembly pathway. The rationale was that subunits with an extensive interface in the final structure assemble early. We tested our method against two existing methods on a data set of 21 proteins with reported assembly pathways. Our prediction outperformed the other methods and ran in feasible runtimes of a few minutes at most.
We also tested our method on respiratory complex I, the respiratory supercomplex and the respiratory megacomplex. We compared the results for the different normalizations with an assembly pathway of respiratory complex I described in the literature. We transformed the assembly pathways to dendrograms and compared the predictions to the reference using the Robinson-Foulds distance and clustering information distance. We analyzed the landscape of the clustering information distance by generating random dendrograms and showed that our result is far better than expected at random. We showed in a detailed analysis that the assembly prediction using one normalization was able to capture key features of the assembly pathway that has been proposed in the literature.
In conclusion, we presented different applications of graph theory to automatically analyze the topology of protein complexes. Our programs run in feasible runtimes even for large complexes. We showed that graph-theoretic modeling of the protein structure can be used to analyze MD simulation data, identify modules of protein complexes and predict assembly pathways.
Recently, carbonates have attracted a lot of attention, due to the recognition of their importance in the global carbon cycle. This was enabled by improvement of the experimental techniques that allow for investigating the stability, structure, and physical properties of materials and high-pressures and high-temperatures, that is, they allow for investigating minerals and geochemical processes at the conditions occurring deep inside Earth. Although a lot of research has been focused on carbonates, there are still some open questions regarding their structure and physical properties at such extreme conditions. The aim of this thesis is to establish a deeper understanding of the nature of the phase transitions in carbonates by studying how do the atoms building up the crystal structure vibrate, that is lattice dynamics. The methodology adapted in this study is a combination of experimental and computational methods which allows for a very thorough examination of the problem. The computational approach allows to determine parameters that are elusive or tedious to measure, and the experimental results provide a solid benchmark for the calculations. This tandem of methods has been widely used for investigating lattice dynamics of various materials. In this study it was used to elucidate the structure and properties of carbonates in the deep Earth conditions
My PhD work employed genetic and pharmacological manipulations, coupled with highresolution live imaging, to understand intercellular communications during zebrafish cardiovascular development. The heart is the first organ to form, and it is composed of several tissues, among which interactions are crucial. I identified two important interactions between muscular and non-muscular tissues in poorly characterized contexts, and the molecules required for the signalling. First, I discovered an important cellular and molecular crosstalk orchestrating the development of the cardiac outflow tract (i.e., the aortic root in mammals).
Endothelial-derived TGF-beta signalling controls the generation of the local extracellular matrix (ECM). The ECM in turn affects endothelial proliferation as well as smooth muscle cell organization (Boezio et al, 2020; Bensimon-Brito*, Boezio* et al, 2020). In my second project, I investigated the crosstalk between the epicardial layer and the myocardial wall. By generating epicardial-impairment models, I identified a novel role for the epicardium in regulating cardiomyocyte volume during heart development (Boezio et al, 2021). Ultimately, this research contributed to our understanding of how paracrine signalling controls the multicellular interactions integral to organogenesis.
In the human brain, the incoming light to the retina is transformed into meaningful representations that allow us to interact with the world. In a similar vein, the RGB pixel values are transformed by a deep neural network (DNN) into meaningful representations relevant to solving a computer vision task it was trained for. Therefore, in my research, I aim to reveal insights into the visual representations in the human visual cortex and DNNs solving vision tasks.
In the previous decade, DNNs have emerged as the state-of-the-art models for predicting neural responses in the human and monkey visual cortex. Research has shown that training on a task related to a brain region’s function leads to better predictivity than a randomly initialized network. Based on this observation, we proposed that we can use DNNs trained on different computer vision tasks to identify functional mapping of the human visual cortex.
To validate our proposed idea, we first investigate a brain region occipital place area (OPA) using DNNs trained on scene parsing task and scene classification task. From the previous investigations about OPA’s functions, we knew that it encodes navigational affordances that require spatial information about the scene. Therefore, we hypothesized that OPA’s representation should be closer to a scene parsing model than a scene classification model as the scene parsing task explicitly requires spatial information about the scene. Our results showed that scene parsing models had representation closer to OPA than scene classification models thus validating our approach.
We then selected multiple DNNs performing a wide range of computer vision tasks ranging from low-level tasks such as edge detection, 3D tasks such as surface normals, and semantic tasks such as semantic segmentation. We compared the representations of these DNNs with all the regions in the visual cortex, thus revealing the functional representations of different regions of the visual cortex. Our results highly converged with previous investigations of these brain regions validating the feasibility of the proposed approach in finding functional representations of the human brain. Our results also provided new insights into underinvestigated brain regions that can serve as starting hypotheses and promote further investigation into those brain regions.
We applied the same approach to find representational insights about the DNNs. A DNN usually consists of multiple layers with each layer performing a computation leading to the final layer that performs prediction for a given task. Training on different tasks could lead to very different representations. Therefore, we first investigate at which stage does the representation in DNNs trained on different tasks starts to differ. We further investigate if the DNNs trained on similar tasks lead to similar representations and on dissimilar tasks lead to more dissimilar representations. We selected the same set of DNNs used in the previous work that were trained on the Taskonomy dataset on a diverse range of 2D, 3D and semantic tasks. Then, given a DNN trained on a particular task, we compared the representation of multiple layers to corresponding layers in other DNNs. From this analysis, we aimed to reveal where in the network architecture task-specific representation is prominent. We found that task specificity increases as we go deeper into the DNN architecture and similar tasks start to cluster in groups. We found that the grouping we found using representational similarity was highly correlated with grouping based on transfer learning thus creating an interesting application of the approach to model selection in transfer learning.
During previous works, several new measures were introduced to compare DNN representations. So, we identified the commonalities in different measures and unified different measures into a single framework referred to as duality diagram similarity. This work opens up new possibilities for similarity measures to understand DNN representations. While demonstrating a much higher correlation with transfer learning than previous state-of-the-art measures we extend it to understanding layer-wise representations of models trained on the Imagenet and Places dataset using different tasks and demonstrate its applicability to layer selection for transfer learning.
In all the previous works, we used the task-specific DNN representations to understand the representations in the human visual cortex and other DNNs. We were able to interpret our findings in terms of computer vision tasks such as edge detection, semantic segmentation, depth estimation, etc. however we were not able to map the representations to human interpretable concepts. Therefore in our most recent work, we developed a new method that associates individual artificial neurons with human interpretable concepts.
Overall, the works in this thesis revealed new insights into the representation of the visual cortex and DNNs...
The heart is the first functional organ that develops in the embryo. To become a functional organ, it undergoes several morphogenetic processes. These morphogenetic events involve different cell types, that interact with each other and respond to the surrounding extracellular matrix, as well as intrinsic and extrinsic mechanical forces, assuming different behaviors. Additionally, transcription factor networks, conserved among vertebrates, control the development.
To have a better understanding of cell behavior during development, it is necessary to find a model system that allows the investigation in vivo and at single-cell resolution. Thanks to the common evolutionary origin of the different cardiac structures, together with the conserved molecular pathways, the two-chambered zebrafish heart offers many advantages to study cell behavior during cardiac morphogenesis. Here, using the zebrafish heart as a model system, I uncovered the cell behavior behind two of the main cardiac morphogenetic events: cardiac wall maturation and cardiac valve formation.
In the first part of this study, I investigated how the cardiac wall is maintained at the molecular level. Using genetic, transcriptomic, and chimeric analyses in zebrafish, we find that Snai1b is required for myocardial wall integrity. Global loss of snai1b leads to the extrusion of CMs away from the cardiac lumen, a process we show is dependent on cardiac contractility. Examining CM junctions in snai1b mutants, we observed that N-cadherin localization was compromised, thereby likely weakening cell-cell adhesion. In addition, extruding CMs exhibit increased actomyosin contractility basally, as revealed by the specific enrichment of canonical markers of actomyosin tension - phosphorylated myosin light chain (active myosin) and the α-catenin epitope α-18. By comparing the transcriptome of wild-type and snai1b mutant hearts at the early stages of CM extrusion, we found the dysregulation of intermediate filament genes in mutants including the upregulation of desmin b. We tested the role of desmin b in myocardial wall integrity and found that CM-specific desmin b overexpression led to CM extrusion, recapitulating the snai1b mutant phenotype. Altogether, these results indicate that Snai1 is a critical regulator of intermediate filament gene expression in CMs and that it maintains the integrity of the myocardial epithelium during embryogenesis, at least in part by repressing desmin b expression.
In the second part of this study, I focused on the behavior of valve cells during cardiac development. Using the zebrafish atrioventricular valve, I focus on the valve interstitial cells which confer biomechanical strength to the cardiac valve leaflets. We find that initially AV endocardial cells migrate collectively into the cardiac jelly to form a bilayered structure; subsequently, the cells that led this migration invade the extracellular matrix (ECM) between the two EC monolayers, undergo an endothelial-to-mesenchymal transition as marked by loss of intercellular adhesion, and differentiate into VICs. These cells proliferate and are joined by a few neural crest-derived cells. VIC expansion and a switch from a pro-migratory to an elastic ECM drive valve leaflet elongation. Functional analysis of Nfatc1 reveals its requirement during VIC development. Zebrafish nfatc1 mutants form significantly fewer VICs due to reduced proliferation and impaired recruitment of endocardial and neural crest cells during the early stages of VIC development. Analysis of downstream effectors reveals that Nfatc1 promotes the expression of twist1b, a well-known regulator of epithelial-to-mesenchymal transition. This study shows for the first time that Nfatc1 regulates zebrafish VICs formation regulating valve EMT in part by regulating twist1b expression. Moreover, it proposes the zebrafish valve as an excellent model to study the cellular and molecular process that regulate VIC development and dysfunction.
In conclusion, my work: 1) identified an unsuspected role of Snai1 in maintaining the integrity of the myocardial epithelium, opening new avenues in its role in regulating cellular contractility; 2) uncovered the function of Nfatc1 in the establishment of the VIC, establishing a new model to study valve development and function.
Anthropogenic interventions have altered all ecosystems around the world. One of those ecosystems are forests, the main resource for timber. They have been strongly transformed in their structure with large consequences on forest biodiversity. Especially the decrease in dead-wood volume due to the timber extraction and alternation of natural forest structures with even-aged stands of less diverse tree species composition has put especially saproxylic, i.e., dead-wood dependent species, under threat, which comprise about 20% of all forest species. Beetles, fungi and bacteria are three functional important groups for decomposition processes but we still lack much information about their sampling and the drivers of their diversity, thus it is difficult to comprehensively protect their diversity. Saproxylic fungi are a highly diverse species group and the main drivers of dead-wood decomposition; hence they play a major role in the global carbon cycle. Due to their cryptic lifestyle, many species are still unknown, but the recent advances in environmental DNA barcoding methods (metabarcoding) shed light on the formerly underestimated diversity. Yet, this method's accuracy and suitability in detecting specific species have not been assessed so far, limiting its current usefulness for species conservation. On the other hand, these methods are a convenient tool to study highly diverse areas with high numbers of unknown species, enabling the study of global diversity and its drivers, which are unknown for saproxylic fungi, but important to assess to predict the future impacts of global change. Since nature conservation concepts are usually not applied on a global scale, the drivers of diversity must also be assessed on smaller scales. Besides understanding the drivers of diversity, to identify focus scales to create comprehensive, evidence-based conservation concepts must utilize multi-taxonomic studies since saproxylic species are differently sensitive towards environmental variables and closely interact with each other. Filling these knowledge gaps is utterly needed to protect the high saproxylic diversity and ensure the functional continuity of decomposition processes, especially regarding the global change.
To address the usefulness of metabarcoding for fungal species conservation, I compared the traditional method of fruit body sampling with metabarcoding and their efficiency in detecting threatened fungal species in the first chapter of this thesis. Both methods have advantages and disadvantages. Their ability to detect threatened saproxylic fungal species and their dependencies on detecting specific fungal groups have not been compared, albeit they are important to inform species conservation like Red Lists properly. I found metabarcoding to generally detect more threatened fungal species than fruit body sampling with a higher frequency than fruit body sampling. Moreover, fruit body sampling detected a unique set of species, while fruit body sampling missed large parts of fungal diversity due to species-specific fruiting characteristics. Metabarcoding with high sampling intensity is thus a viable method to assess threatened saproxylic fungal diversity and inform nature conservation like Red Lists about distribution and abundances. Nevertheless, a complementary approach with fruit body sampling is indispensable for assessing all threatened fungal species.
In order to analyse the global diversity of saproxylic fungi and its drivers, I examined whether fungal species richness increases from the poles towards the equator and thus follows the latitudinal diversity gradient already found in many other species groups. I further investigated whether such an increase is caused by increasing ecological specialisation, i.e., niche partitioning, or local tree diversity, i.e., niche space. Gamma diversity per biome increased from the boreal, over the temperate to the tropics and thus confirmed the latitudinal diversity for saproxylic fungi. Contrastingly, alpha diversity at the log level did not significantly increase towards the tropics, suggesting a grain size dependency of the observed pattern and an equal niche space within dead-wood across latitudes. Ecological specialisation on the plot level was globally on a high level but did not increase significantly towards the equator. Additionally, I found local tree species richness to drive plot-based fungal diversity. Further analysis of gamma diversity against the total number of sampled tree species strengthened the assumption that tree species diversity and not increased ecological specialisation was the main driver of the latitudinal diversity gradient, as there was no significant difference between the gamma diversity of the temperate and tropical biome. Nonetheless, as the gamma diversity of the boreal biome was still significantly smaller, my results do not allow a complete neglection of the ecological specialisation hypothesis. The overall results indicate a strong dependency of saproxylic fungi diversity with host tree species diversity and that the global loss of tree species threatens saproxylic fungi with an unpredictable impact on carbon and nutrient cycling.
To support saproxylic conservation, I conducted two analyses. First, I compared the beta diversity of the three main decomposer groups (beetles, fungal fruit bodies, mycelial fungi (metabarcoding), and bacteria (metabarcoding)) across different scales to assess the impact of different environmental variables on their overall diversity. I used an experimental design to disentangle two different spatial scales, influenced by differences in macroclimate, forest microclimate and spatial distance, and two host scales, driven by differences between tree lineages and tree species. I set these beta diversities in relation to the gamma diversity of the three main decomposer groups to identify whether a unified conservation concept could be applied to one scale to optimally protect the diversity of all three species groups. Second, I identified whether diversity and community composition of fungi and bacteria differed among climate and land use gradients. Further I explored whether specialisation and niche packing could explain the expected pattern. To do so I used an experimental design disentangling climate and land use across a large gradient in Germany. The results differed among the species groups, denying a unified conservation concept focusing on one scale. Saproxylic beetle and fruit body beta diversity was equally high on each scale, as they are more sensitive towards environmental factors like macro- and microclimate. On the other hand, mycelial fungi and bacteria beta diversity was highest on the host scale, especially the host tree scale, indicating a high host specificity of the two groups. The second study also identified tree species as the main driver of diversity and community composition of these two study groups. Specialisation of fungi was not influenced by land use or climate. Bacterial specialisation and diversity were under a strong influence of mean precipitation. Comprehensive conservation of multi-taxonomic diversity across regions thus requires the integration of several scales. Within different macroclimatic regions, forests of varying microclimates, i.e., forest management, must be implemented. In these forests, dead-wood of different tree lineages, i.e., angio- and gymnosperms and tree species, must be provided.
Taken together, I could demonstrate that metabarcoding is an efficient method to sample threatened fungal species and identify differing drivers of fungal diversity present as fruit bodies or mycelium. Its usefulness will further increase due to the ongoing improvement of sequencing databases and thus better inform conservation concepts. Using metabarcoding, I could demonstrate that high host specialisation of saproxylic fungi is not a European but a global phenomenon and identify tree species loss under global change as one major concern for saproxylic diversity. My dissertation further highlighted the importance of multi-taxonomic studies for evidence-based nature conservation, as different species groups require varying concepts. These results were especially important for saproxylic bacteria as the drivers of their diversity are still largely unknown. Howbeit, large research gaps still exist regarding the impacts of global change on species and processes. Moreover, the spatial coverage of studies is needed to confirm or neglect the generality of current research especially concerning the highly diverse tropical areas. An increased focus on the drivers of diversity in these areas is crucial to ensure a globally comprehensive saproxylic conservation and the various ecosystem functions they control.
To gain a better understanding of complex mechanisms in biological systems, simultaneous control over multiple processes is key. To this purpose selective photouncaging has been developed. Photo-uncaging is an experimental scheme in which a molecule of interest has been inactivated synthetically and is activated by light. Usually a bond is cleaved and a leaving group is set free. The molecule which inactivates the molecule of interest and sets the leaving group free is called (photo-)cage. In a selective photo-uncaging scheme a number of leaving groups can be released independently, usually by irradiation with light of different wavelengths. This approach is, however, seriously limited in its applicability due to the properties of the involved cages and irradiation schemes. A major drawback is the usually quite broad UV-Vis absorption of the cages. This makes a selective activation by light difficult and limits the maximal number of independent cages severely.
Therefore, the aim of this thesis is to introduce the Vibrationally Promoted Electronic Resonance (VIPER) 2D-IR pulse sequence in a alternative selective uncaging scheme.
The VIPER 2D-IR pulse sequence is a spectroscopic tool which allows to generate 2D-IR signals whose lifetime are independent of the vibrational relaxation lifetime. It has been first used to monitor chemical exchange. It consists of a narrowband infared pump pulse, a subsequent UV-Vis pump pulse and a broadband infrared probe pulse. The UV-Vis pump pulse is off-resonant with regard to the UV-Vis absorption band. Electronic excitation becomes only possible, if the infrared pump pulse modulates the UV-Vis transition of the IR-excited molecule. This modulation brings the UV-Vis transition in resonance with the UV-Vis pump pulse. Thereby, only the molecules which were pre-excited with the infrared pulse can be excited into the electronically excited state. A computational prediction of the modulation was carried out by Jan von Cosel in the Burghardt group.
The narrowband infrared pump pulse can be used to selectively excite a subensemble of molecules in a mixture into an electronically excited state even if the UV-Vis spectra of all molecules are virtually identical. For this the sub-ensemble needs to exhibit an identifiable infrared spectrum. Combined with the introduction of isotope labels, which lead to changes in the infrared absorption spectra, the larger selectivity in the infrared region can be exploited for an alternative selective uncaging approach. In VIPER uncaging the infrared pump pulse selects the species and the subsequent UV-Vis pulse provides the energy needed for electronic excitation upon which the photo cleavage can occur.
After an introduction of the principle idea of uncaging and VIPER spectroscopy, the concept of VIPER uncaging is introduced and its limits and requirements are discussed. Some examples for possible VIPER cages are reviewed.
A coumarin molecule (7-diethylamino coumarin) which can release an azide group was chosen as a first test molecule for VIPER uncaging. Its isotopomers were characterized to determine suitable spectroscopic markers for successful uncaging and to find fitting experimental conditions. The chosen coumarin cage has an UV-Vis absorption band at approximately 380 nm and a steep flank on the high wavelength side of the band. The quantum yield for the azide compound is between 10-20 % depending on the solvent’s water content. The release was found to be on a picosecond timescale which is among the fastest known photo reactions, but the photo reaction mechanism has proven to be not straightforward. For the VIPER experiment on the mixture two isotopomers were chosen with a 13C atom at different positions. In one species a ring mode of the coumarin is changed by the 13C atom. In the other isotopomer the carbonyl stretching mode is influenced. The change in the ring mode region allows to select one species or the other with the infrared pre-excitation. Because of experimental difficulties only isotopomers with the same leaving group could be used. The successful selective electronic excitation of the individual isotopomers in a mixture was monitored by probing the carbonyl region.
As a second VIPER cage, para-hydroxyphenacyl (pHP) was chosen. A thiocyanate group was selected as leaving group. pHP cages have their electronic transition in the UV, with a maximum absorption at 290 nm. The shape of the spectrum is suitable and the quantum yield is very high, with values in the literature of up to 90 %. Also the photo reaction is well studied and the expected byproducts are well characterized. The chosen isotopologues were characterized spectroscopically. The resulting data on the photo reaction were in agreement with the mechanism proposed in the literature. The mixture for the VIPER experiment consisted of two isotopologues, where for one species all the C atoms in the ring were labelled and for the other the C-atom in the thiocyanate leaving group was labelled. Here the release of the different leaving groups, labelled and unlabelled thiocyanate, could be monitored selectively. This shows that it is possible to selectively release a molecule in a mixture of caged molecules by applying the VIPER pulse sequence.
The samples were synthesized by Matiss Reinfelds from the Heckel group and the VIPER experiments were done together with Carsten Neumann and with support
of the Bredenbeck group.
The leaving groups were chosen because of their infrared absorption which allowed to directly monitor the successful cleavage by spectroscopy. This was needed for the proof-of-concept experiment and to allow direct optimization of the experimental parameters but is not necessarily a requirement for VIPER uncaging.
Concerning the selectivity of the VIPER uncaging, the approach is at the moment mainly limited by the infrared pulse energy. The selective VIPER excitation is competing with unselective excitation directly by just the UV-Vis pulse. A more intense infrared pump pulse would increase only the selective VIPER excitation and thereby improve the contrast to the unspecific background.
To address this issue, the first steps towards an alternative infrared light generation are undertaken. In this alternative approach the infrared light for preexcitation is directly generated by difference frequency generation of the laser output, i.e. the high energy 800 nm fundamental, and the output of a non-collinear optical parametric amplifier (NOPA). To achieve a narrowband pump pulse the pulses are chirped before mixing. In the scope of this thesis a NOPA has been installed and the mixing has been tested with available test crystal medium. While infrared wavelength region and power were not in the aspired range with this alternative crystal the feasibility of mixing between a NOPA output and the fundamental could be shown.
Other possibilities to increase the contrast to the unspecific background excitation by the UV-Vis pump pulse are discussed. For most applications of selective VIPER uncaging the detection by fs-laser spectroscopy will not be needed and could be replaced by other methods e.g. chromatography. This will allow the experimental parameters of the VIPER pulse sequence to be changed in a way which reduces unspecific excitation i.e. reducing the UV-Vis-pump energy and result in much better contrast.
In conclusion, the experimental data in this thesis shows the VIPER pulse sequence to be applicable to selective uncaging schemes and indicates measures to arrive at the specificity necessary for uncaging applications. This thesis was focused on uncaging photo reactions with isotopomers and isotopologues, but other types of photo reactions could in principle be controlled in the same way. It should be possible to address different isomers in mixtures or different ground states of proteins selectively. The discussed experiments are a significant step towards control over photo reactions in mixtures.
Uncaging approach, native membrane dynamics and lipidic cubic phases in biomolecular solid-state NMR
(2019)
It was previously shown for the Escherichia coli diacylglycerol kinase (DgkA) that enzyme-reactions at the membrane interface can be monitored by solid-state NMR. However, such studies can face problems due to limited accessibility of the active sites: Natural substrates for membrane enzymes, but also ligands for membrane proteins or lipid mediators, are either partitioning into the membrane and cannot be added easily, or if soluble exhibit accessibility restrictions, as they cannot freely pass through lipid bilayers. This situation complicates quantitative kinetic analysis of biochemical processes such as enzyme activity, ligand binding, but also oligomerization or folding reactions in the membrane or at its interface under MAS NMR conditions.
To overcome these limitations the feasibility and possible advantages of the uncaging approach as a new tool for biomolecular solid-state NMR to trigger reactions by light have been explored. DgkA’s enzymatic activity, exemplary of a biochemical process on the membrane interface, was thereby triggered in situ during MAS by light-induced release of its substrates that were rendered inactive with photolabile protecting groups. To be capable of uncaging sufficient amounts of substrate during MAS to follow the enzymatic reaction via 31P real-time NMR measurements, several illumination variants including an existing illumination setup to study retinal proteins under cryogenic conditions via DNP enhanced NMR were tested. As uncaging of micromole amounts of substrates requires a higher flux compared to initiation of a photocycle in retinal proteins, a new illumination setup was built with Bruker Biospin and Leoni Fibertech. It consists of a modified MAS probe and a suitable fiber bundle, allowing to efficiently couple light from high power LEDs into a sapphire rotor containing the sample, without disturbing the magnetic field homogeneity or sample rotation. By reducing the sample volume to the illuminated area up to 60 mM ATP were released by uncaging NPE ATP to initiate DgkA’s activity in several tested membrane mimetics. These mimetics included liposomes and bicelles, which are well established in the field of biomolecular solid state NMR as well as the optically transparent lipidic cubic phase of monoolein, widely used in membrane protein crystallography, but not yet well characterized as membrane mimetic under MAS conditions. A unique and powerful but compared to time and spatial resolution often underrepresented advantage of the uncaging approach for biophysical studies has been demonstrated by successful uncaging of a non-miscible lipid substrate to trigger DgkA’s kinase reaction: Initiation of processes that cannot easily be triggered by mixing. Examples of these are reactions involving highly hydrophobic, membrane partitioning compounds including lipid substrates, ligands or interaction partners, but also oligomerization or folding of biomacromolecules. The herein performed experiments therefore serve as a first demonstration of the uncaging approach’s feasibility and compatibility with a wide variety of membrane mimetics and give a first indication of its potential for a variety of biomolecular solid state NMR experiments.
As high accessibility for solutes has been a second focus for the choice of membrane mimetics, DgkA’s activity in the lipidic cubic phases of monoacylglycerols with its two continuous networks of water channels has been further characterized. Kinetic parameters obtained from 31P real time solid state NMR experiments revealed that DgkA’s activity is similar to activities obtained in swollen cubic phases in a bath solution with wider water channels. Diffusion of ATP in a non swollen cubic phase was however strongly reduced compared to ATP in solution as diffusion measurements showed. Therefore, saturation of the enzyme required distinctly higher ATP concentrations. These results thereby underline the advantage of a non invasive and label free method like NMR to directly gain information about enzymatic reactions of immobilized enzymes in porous materials. The obtained wealth of information from 31P real time NMR experiments and biochemical assays in different membrane mimetics in presence and absence of lipid substrates and activators also provided further insight into DgkA’s enzymatic activity. It confirms ATP binding and hydrolysis in the absence of a lipid substrate, in agreement with the proposed mode of substrate binding, and allowed to estimate the in vivo relevance of previously observed ATPase activity in liposomes.
Further exploration of the cubic phase as membrane mimetic for protein solid state NMR revealed its high stability under MAS at elevated temperatures and capacity to reconstitute sufficient amounts of DgkA. Unlike monoolein, DgkA was cross-polarizable in a cubic phase and exhibited similar dynamics compared to DgkA reconstituted into liposomes, allowing to acquire the herein shown dipolar coupling based 2D protein spectra. As lipidic cubic phases are not containing phospholipids, monoacylglycerols could be especially useful as membrane mimetics for 31P correlation spectra. Initial experiments under DNP conditions, where in liposomes line broadening causes severe overlap of phospholipid signals and unspecific cross polarization highlight this aspect.
In summary, herein reported results of the experiments performed with lipidic cubic phases demonstrate that they are robust and versatile membrane mimetics. They could be of advantage for a variety of solid-state NMR experiments where either optical transparency for efficient illumination is desired, accessibility for solutes and membrane components under MAS is required, or interference of phosphorous signals of other membrane mimetics must be avoided.
In the second chapter of this thesis 1H solid-state NMR as a label free method to probe membrane order and dynamics directly within a cellular and disease relevant context was used to observe the effects of soluble epoxide hydrolase (sEH) encoding gene knock-outs on membrane dynamics. Knock-out of the sEH encoding gene changed the overall membrane dynamics in the physiological temperature range of native membranes derived from mouse brains, making the bulk membrane more dynamic. To confirm that these effects are related to the enzymatic activity of sEH, substrates and products of sEH were added to evaluate their effects on membrane dynamics. 19,20 dihydroxydocosapentaenoic acid (DHDP), a product of sEH, partially reversed the knock out phenotype in a concentration dependent manner whereas the substrate 19,20 epoxydocosapentaenoic acid did not cause any effects. As both polyunsaturated fatty acids did not show differences in phase behavior in a simple phospholipid bilayer these results provide evidence that the previously observed concentration dependent DHDP induced relocation of cholesterol away from detergent resistant lipid raft fractions is associated with alteration of membrane dynamics. Therefore, also the effect of cholesterol removal via cyclodextrin on membrane dynamics was analyzed. Removal of cholesterol led to a similar temperature profile of wild type and knock out membranes thereby supporting the hypothesis that DHDP induced relocation of cholesterol is causing altered membrane dynamics. These alterations have been shown by the lead authors of the collaborative research project to induce relocation of various membrane proteins and are involved in the development of diabetic retinopathy. Furthermore, in this context inhibition of sEH has been shown to inhibit diabetic retinopathy and proposed as target for prevention of one of the leading causes of blindness in the developed world.
In der modernen Festkörperphysik spielen elektronisch stark korrelierte Systeme mit ihrem komplexen Vielteilchenverhalten eine zentrale Rolle. Insbesondere das Wechselspiel zwischen thermischen und Quantenfluktuationen in den Ladungs- und Spinfreiheitsgraden führt zur Entstehung verschiedenster neuartiger Grundzustände.
Die vorliegende Dissertation „Ultrasonic and Magnetic Investigations in frustrated Lowdimensional Spin Systems“ beschäftigt sich mit den besonderen physikalischen Eigenschaften niedrig dimensionaler Spinsysteme. Diese Materialklasse, die auch zu den stark korrelierten Systemen zählt, wird seit vielen Jahren intensiv sowohl experimentell als auch theoretisch untersucht. Auf theoretischer Seite sind die niedrigdimensionalen Spinsysteme besonders interessant, da sie als Modellsysteme die exakte Beschreibung des Grundzustandes und des Anregungsspektrums ermöglichen. Von experimenteller Seite ist es in den letzten Jahrzehnten gelungen, verschiedenste Materialklassen niedrigdimensionaler Spinsysteme zu synthetisieren.
In der vorliegenden Arbeit werden die grundlegenden Theorien und physikalischen Konzepte niedrigdimensionaler Spinsysteme diskutiert. Insbesondere auch die Spin-Phonon-Wechselwirkung dieser Materialien, die für die hier beobachteten elastischen Anomalien verantwortlich ist. Weiterhin wird auch das elastische Verhalten bei magnetischen Phasenübergängen beschrieben.
Da die Ultraschallexperimente einen Schwerpunkt dieser Arbeit bilden, wird der Versuchsaufbau zur phasenempfindlichen Detektion von Schallgeschwindigkeit und Ultraschalldämfung ausführlich beschrieben. Diese Messmethode ist ideal zur Untersuchung der Spin-Phonon Wechselwirkung geeignet.
A new experimental setup, for pump-probe fs DFWM measurements, which is based on a femtosecond laser system, has been constructed. It allows for the investigation of molecular species in the gas phase at different temperatures, from ~30 K in a seeded supersonic jet up to ~500 K in a heat-pipe oven. In comparison to other RCS methods the employed fs DFWM technique is less complicated and gives much higher signal-to-noise ratio [BFZ86, FeZ95a, CKS89, CCH90, HCF91, WRM02, Rie02]. A general computer code for the simulation of fs DFWM spectra of nonrigid asymmetric top molecules has been developed. This new DFWM code in combination with a non-linear fitting routine allows one to determine rotational and centrifugal distortion constants and obtain information on the polarizability tensor components from the experimental spectra. Fs DFWM spectroscopy was successfully applied to the medium-sized molecules benzene and benzene-d6 in a gas cell and in a supersonic jet. The spectrum from a seeded expansion has been measured up to delay time of 3.9 ns (restricted by the length of the delay stage) with excellent signal-to-noise ratio (102-103). In that way 87 and 72 J-type transients have been recorded for benzene and benzene-d6, correspondingly. A relative accuracy on the order of 10-5 has been achieved for the rotational constant. From the room temperature experiments, precise values of centrifugal distortion constants DJ and DJK have been extracted. The literature data for cyclohexane have been revised and a new precise rotational constant B0 has been obtained, which is (+5.5 MHz) shifted from the one reported in the former Raman investigation by Peters et al. [PWW73]. Additionally, high-level ab initio calculations of cyclohexane have been carried out using a large number of basis sets at several levels of theory. In particular, the vibrational averaging effects have been examined in order to critically compare the experimentally determined and theoretically evaluated rotational constants. The contribution of highly symmetric vibrational modes to vibrational averaging effects was clarified. More structural information could be obtained from fs DFWM measurements of asymmetric top species, since different type of rotational recurrences can appear, and all three rotational constants (A, B, C) can be extracted. On the other hand the analysis of the asymmetric top spectra is no longer trivial. In fact the simple formula for rotational recurrence periods of symmetric top species (Tab. 2.1) can not be applied to asymmetric top molecules. Thus, in order to extract high-resolution data for asymmetric species, a complete fitting of the experimental spectra is necessary. The fs DFWM and (1+2') PPI method have been applied to the asymmetric top molecules pyridine in the ground (S0) and pDFB in the S0 and electronically excited (S1) states. By fitting the measured fs DFWM spectra the rotational and centrifugal distortion constants have been extracted with good precision and the value of the parametrized polarizability angle of pDFB was obtained. In this work, the first application of fs DFWM spectroscopy to a molecular cluster has been reported. Also, the chemical equilibrium between monomeric and dimeric species was studied. In particular formic and acetic acid have been investigated in a gas cell and in a supersonic expansion. Many spectral features have been observed and analized in the fs DFWM spectrum of formic acid vapor in a gas cell at room temperature. Most of them were attributed to rotational recurrences of the formic acid monomer, but also spectral feature originating from the formic acid dimer of O-H×××O/O×××H-O type have been detected and analyzed. From the fitted simulation, the rotational and centrifugal distortion constants, and parametrized polarizability angle were extracted for the dimeric structure of O-H×××O/O×××HO type. With the assumption of unperturbed monomers a center-of-mass distance of R = 2.990 ± 0.001 Å for the monomers within the dimer has been calculated from the spectroscopic results. This distance is 0.028 Å smaller than that reported from electron diffraction [ABM69]. Thus, the centers-of-mass distance was assigned as the main point of disagreement between results of fs DFWM and electron diffraction experiments. In contrast to formic acid, acetic acid shows strong recurrences from dimeric species even in the fs DFWM spectra at room temperature. This is explained in terms of different symmetry of the moments-of-inertia tensor, which modulates the intensity of RRs (the fs DFWM signal is in general stronger from symmetric species). Due to the symmetric nature of the acetic acid dimer, only the sum (B+C) of the rotational constants has been extracted. The changes of geometrical parameters upon dimer formation have been analyzed for, both, formic and acetic acid. A heat-pipe oven has been used in order to overcome the main drawback of fs DFWM spectroscopy – the square dependence of the signal intensity on the sample number density. Two-ring molecules (cyclohexylbenzene, para-cyclohexylaniline and nicotine) with low vapor pressure (<0.1 mbar) at room temperature have been investigated. From the analysis of the experimental and ab-initio results for CHB and pCHA a nearly perpendicular conformation of the aromatic vs. cyclohexane ring for both system is inferred. The enlargement of the benzene ring of CHB in the electronically excited state (S1) has been found to cause the smaller rotational constants in S1. This conclusion has been drawn from the comparison of the ground and electronically excited state experimental rotational constants in combination with ab-initio calculations. The extraction of precise structural information for nicotine was not possible due to it weak fs DFWM signal. However, the fact that fs DFWM technique can be applied to conformational analysis of molecular species in an equilibrium mixture opens other applications for this kind of spectroscopy. In general the results obtained in this work show that the fs DFWM technique, being an experimental implementation of RCS, provides one with an important tool for structural analysis of molecular species in the gas phase in particular for the species to which microwave spectroscopy can not be applied. It gives spectra with excellent signal-to-noise ratio even at low number density samples expanded in a seeded supersonic jet. It provides an alternative and innovative approach towards rotational Raman spectroscopy of large polyatomic molecules applicable under various experimental conditions (broad temperature and pressure range). With the introduction of femtosecond (10-15s) laser pulses (usually picosecond (10-12s) laser pulses were used in RCS) an improvement in time-resolution and therefore in precision for the rotational constants by more than one order of magnitude has been achieved. Molecular systems in the ground electronic state without permanent dipole moment and chromophore can be studied with high precision, providing thereby molecular benchmark systems for the electronic structure theory. As has been shown, the study of molecular clusters by fs DFWM spectroscopy is possible, but its potential are restricted by the square dependence of the fs DFWM signal from the sample number density, which is even more important for supersonic jet expansions. Here, the application of near-resonant and resonant FWM schemes should help in order to compensate for the low sample concentration. With the introduction of the heat pipe oven for fs DFWM experiments, the investigation of large nonvolatile molecules under equilibrium conditions is possible now. In our laboratory the first results on the structural analysis of different conformers of pyrrolidine in the gas phase have been obtained [MaR04]. This method can have even more prospects for the structural investigations of large molecular species in combination with new non-thermal gas phase sources for nonvolatile molecules, like laser desorption [CTL89], laser oblation [MHL83], electrospray [FMM90], laser induced liquid beam ion desorption [KAB96, Sob00] etc. A very recent application of the fs DFWM technique is the investigation of the influence of strong laser fields on molecular gas phase sample, which could range from active alignment [PPB03] over molecular deformation to field ionization [CSD03]. In regards to future development in fs DFWM spectroscopy for more complex molecules one has to take into account, how large amplitude motions such as the van der Waals vibrations or internal rotation (see section 6.4.2) affect the rotational coherences. In any case, femtosecond Degenerate Four-Wave Mixing as experimental implementation of Rotational Coherence Spectroscopy can be considered as an innovative, developing, and powerful method for the structural investigation of the molecular species, which are hard to study by classical frequency-resolved spectroscopy [FeZ95a, Dan01, Rie02].
Photoinduzierte Energietransferprozesse und -reaktionen spielen in vielen Gebieten von Chemie, Physik und Biologie eine wichtige Rolle. Zu den prominentesten Beispielen zählen der Lichtsammelprozess in der Photosynthese und der Anregungsenergietransfer in funktionellen Materialien. Der Fokus dieser Arbeit liegt auf letzterem Bereich, genauer auf organischer Elektronik und flexiblen Donor-Akzeptor-Bausteinen und Schaltern. Im Besonderen werden hier zwei verschiedene Typen von funktionellen organischen Systemen betrachtet: zum einen oligomere Fragmente organischer halbleitender Polymere wie Oligo-p-Phenylen-Vinylen (OPV) und Oligo-Thiophen (OT), welche als Bausteine für neuartige organische Solarzellen dienen, und zum anderen kleine funktionelle Donor-Akzeptor-Einheiten wie Dithienylethen-Bordipyrromethen (DTE-BODIPY). Letzteres wurde in Kooperation mit den experimentellen Gruppen von K. Rück-Braun (TU Berlin) und J. Wachtveitl (Goethe Universität) untersucht. Um die relevanten Energietransfermechanismen genauer zu verstehen, wurden an diesen Systemen elektronische Strukturrechnungen und quantendynamische Untersuchungen durchgeführt. Hierzu wurden mittels ab initio-Methoden Modell-Hamiltonians parametrisiert und mit hochdimensionalen quantendynamischen oder semiklassischen Methoden kombiniert. Während die Parametrisierung für kleinere Fragmente durchgeführt wurde, lässt sich der so parametrisierte Hamiltonian ohne Weiteres auf größere Systeme erweitern. Die dynamischen Studien der betreffenden Systeme wurden mittels der Multikonfigurationellen Zeitabhängigen Hartree (MCTDH) Methode durchgeführt, welche eine vollständige quantendynamische Beschreibung des Systems zulässt. Für größere Systeme wurde die semiklassische Ehrenfest Methode in Verbindung mit dem Langevin-Ansatz zur Beschreibung von Umgebungseffekten genutzt. Hierzu wurde ein eigens für diese Methode und Systeme geschriebenes Programm eingesetzt. Im Falle der OT- und OPV-Oligomere wurde die Dynamik bei Vorliegen eines strukturellen Defekts untersucht. Ziel war es hierbei, die dynamischen Phänomene, welche durch die Photoanregung induziert werden, zu untersuchen. Des Weiteren wurde untersucht, ob das Konzept von „spektroskopischen Einheiten“, welche die Lokalisierung der Anregung durch strukturelle Defekte beschreibt, in diesen Systemen zutrifft. Hierzu wurden die Systeme in einer Frenkel-Basis definiert, welche ein auf einem Monomer lokalisiertes Elektron-Loch-Paar beschreibt. Delokalisierte elektronische Anregungen können somit als Superposition solcher Frenkel-Zustände beschrieben werden. Neben der Frenkel-Basis wurde aber auch eine verallgemeinerte Elektron-Loch-Basis verwendet, welche über zusätzliche Ladungstransferzustände eine räumliche Separation von Elektronen und Löchern erlaubt.Die Parametrisierung des OPV- und OT-Hamiltonians erfolgte mittels der Algebraischen Diagrammatischen Konstruktions (ADC(2))-Methode, welche in Kombination mit einer Übergangs-Dichte-Matrix-Analyse eine sehr akkurate Beschreibung der Frenkel- und Ladungstransferzustände basierend auf den supermolekularen Zuständen erlaubt. Um vibronische Effekte auf die Dynamik miteinzubeziehen,wurden nieder- und hochfrequente Torsions- und alternierende Bindungslängenmoden des Systems im Hamiltonian berücksichtigt. Hierzu wurden eindimensionale Schnitte der Potentialflächen entlang dieser Koordinaten berechnet und mittels einer Transformation in diabatische Potentialflächen überführt. Mit diesem Setup wurden die quantendynamischen und semiklassischen Simulationen für ein OPV/OT-Hexamer und ein 20-mer durchgeführt. Die Ergebnisse dieser Simulationen zeigen, dass der Energietransfer auf einer Subpikosekunden-Zeitskala stattfindet und eine starke Abhängigkeit vom Vorliegen eines strukturellen Defekts aufweist. Des Weiteren konnte auf einer Zeitskala von 100 Femtosekunden eine Lokalisierung des Exzitons beobachtet werden. Fluktuationseffekte werden zudem über Quantenfluktuationen im Falle von MCTDH bzw. über thermische Fluktuationen im Falle des Ehrenfest-/Langevin-Ansatzes berücksichtigt. Letzterer ist jedoch nicht in der Lage, die kohärente Charakteristik der mit den Schwingungsmoden gekoppelten Exziton- und Lokalisierungsdynamik wiederzugeben. Dagegen kann dieser Ansatz erfolgreich genutzt werden, um eine fluktuationsgetriebene „Hopping“-Dynamik des quasi- stationären Zustandes auf einer längeren Zeitskala in Abhängigkeit von der Temperatur zu beschreiben. Die Beschreibung der Photodynamik der DTE-BODIPY-Dyade zielt darauf ab, experimentell beobachtete vibrationelle Schwingungen des BODIPY-Fragments zu erklären, die ohne eine direkte Anregung dieses Fragments zustande kommen. Diese wurden nach einer selektiven Anregung des DTE-Fragments in zeitaufgelösten UV/Vis Anreg-Abtast-Experimenten beobachtet. Der Fokus der Untersuchung liegt daher auf der Beschreibung der photoinduzierten intramolekulare Energieumverteilung (IVR) auf einer Subpikosekunden-Zeitskala. Die DTE-BODIPY Dyade wurde mittels eines Hamiltonians, welcher durch TDDFT Rechnungen parametrisiert wurde, dargestellt. Basierend auf den Normalmoden des Systems, wurden lokale DTE- und BODIPY-Moden konstruiert, wobei einige dieser Moden miteinander gekoppelt sind und die Photoanregung des DTE auf das BODIPY-Fragment übertragen. Hierbei zeigte sich, dass die Zeitskala und die charakteristischen Frequenzen des Experiments mittels der hochdimensionalen MCTDH-Methode gut reproduziert wurden. Aus den Simulationen ergab sich zudem, dass der beobachtete Energietransfer stark von einem Reservoir von vibrationell angeregten lokalen DTE-Moden beeinflusst wird. Der untersuchte IVR- Prozess zeigt zudem eine ausgeprägte Abhängigkeit von lokalen Kopplungen und der Kopplung an eine Umgebung.
In the last twenty years, there has been splendid progress in energy conversion technologies to have sustainable energy sources. For example, solar cells contribute significantly to energy production as the sun is an enormous source for renewable energy. Currently, the most common commercialized photovoltaic devices are silicon-based. The scientists' main targets are high efficiency, low cost, environmentally friendly, and easy to synthesize new semiconductor materials to replace silicon. Furthermore, understanding the photophysical properties of these materials is very important for designing high efficient photoconversion systems.
This thesis investigates the photophysics of lead-based wide-bandgap perovskites with different dimensionality (2D, 3D) and how they can be optimized for optoelectronic applications. In chapter 1, we present the background and progress in perovskite research. The basic concepts of semiconductor and spectroscopic methods of the applied techniques in this work are discussed in chapter 2.
In the first project (chapter 3.1), we used our time-resolved techniques to study the ultrafast dynamics of energy transfer from the inorganic to the organic layer in a series of three lead-based mixed-halide 2D perovskites containing benzyl ammonium (BA), 1-naphthyl methyl ammonium (NMA), and 1-pyrene methyl ammonium (PMA) thin films.
In the second project (chapter 3.2), we used time-resolved spectroscopic techniques to study the effect of adding 5% of Cs on the dynamics of a mixed-cation wide bandgap bromide-based 3D perovskite.
In another side project (chapter 4), we present the photophysics properties of newly synthesized new Schiff bases containing indole moieties using piperidine as an organic base catalyst and Au@TiO2 as a heterogeneous catalyst. Finally, the results of this work are summarized in Chapter 5 with an outlook and a discussion of open questions for further research.
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.
Ubiquitylation is a three-step process, which results in the attachment of the small protein ubiquitin (Ub) to lysine residues on a substrate protein. SUMO proteins are ubiquitin (Ub)-related modifiers implicated in the regulation of gene transcription, cell cycle, DNA repair and protein localization. The molecular mechanisms by which the sumoylation of target proteins regulates diverse cellular functions remain poorly understood. During my PhD I isolated and characterized SUMO1 and SUMO2 binding motifs. Using Yeast Two Hybrid system, bioinformatics and NMR spectroscopy we defined a common SUMO-interacting motif (SIM) and map its binding surfaces on SUMO1 and SUMO2. This motif forms a β-strand that could bind in parallel or anti-parallel orientation to the β2-strand of SUMO due to the environment of the hydrophobic core. A negative charge imposed by a stretch of neighboring acidic amino acids and/or phosphorylated serine residues determines its specificity in binding to distinct SUMO paralogues and can modulate the spatial orientation of SUMO-SIM interactions. Mutation of the SUMO interacting motif of TTRAP (TRAFS and TNF receptor associated protein) influences both its localization and dynamic behaviour in living cells. Ubiquitin (Ub)-binding domains (UBDs) are key elements in conveying Ub-based cellular signals. UBD-containing proteins interact with ubiquitylated targets and control numerous biological processes including receptor trafficking, DNA repair, virus budding and gene transcription. They themselves undergo UBD-dependent monoubiquitylation, which promotes intramolecular binding of the UBD to the attached Ub and consequently leads to their functional inhibition. During the second part of my PhD I could show that, in contrast to the established ubiquitylation pathway, the presence of UBDs allows the monoubiquitylation of host protein independently of classical E3 ligases. UBDs of different types including UBA, UIM, UBM, NFZ and UBZ, can directly cooperate with E2 Ub-conjugating enzymes to promote monoubiquitylation of their host proteins. Using FRET technology I verified that the E2 enzyme and the substrate directly interact in cells. Moreover, UBD-containing proteins Stam2 and Sts2 promote self-ubiquitylation and not ubiquitylation of other targets or form polyUb chains from free Ub. Our study revealed a yet unappreciated role of E2 enzymes in ubiquitylation reactions of UBD containing proteins.
Ein wesentliches Ziel der Physik mit schweren Ionen ist die Untersuchung der Zustände von Kernmaterie bei hohen Dichten bzw. Temperaturen. Solche Zustände lassen sich durch Kollisionen von hochenergetischen schweren Ionen in Teilchenbeschleunigern wie dem Super Proton Synchrotron SPS am Europäischen Kernforschungszentrum CERN in Genf erzeugen und untersuchen. Die vorliegende Arbeit beschäftigt sich mit der Analyse des Einflusses des in einer solchen Kollision erzeugten Mediums auf hochenergetische Teilchen, welche dieses Medium durchqueren. Hierzu werden Korrelationen zwischen Teilchen mit hohem Transversalimpuls pt als Funktion der Zentralität der Kollisionen und der Ladung der beteiligten Teilchen untersucht. Ziel ist es, hierdurch eine experimentelle Grundlage für die theoretische Beschreibung der Eigenschaften des Mediums in solchen Kollisionen bereitzustellen. ...
Die Physik beschäftigt sich seit jeher mit der Frage nach dem Aufbau und der Struktur der Materie. Die Antworten änderten sich im Laufe der Zeit, der gegenwärtige Stand der Erkenntnis ist im sogenannten Standardmodell zusammengefasst. Dort werden die Elementarteilchen in Leptonen und Quarks unterteilt, die Wechselwirkungen zwischen ihnen beschreibt man durch vier fundamentale Kräfte: die Gravitation, die elektromagnetischen Kraft, die schwache und die starke Kernkraft. Gemäß dem Standardmodell sind Nukleonen, also Protonen und Neutronen, aus Quarks aufgebaut. Das Proton ist beispielsweise ein gebundener Zustand aus zwei up und einem down Quark. Die Nukelonen bilden ihrerseits die Atomkerne, welche die Systematik der Elemente bestimmen. Quarks treten in sechs verschiedenen Arten (flavours) auf: up, down, strange, charm, bottom und top. Freie Quarks konnten bislang nicht nachgewiesen werden, sie werden nur als Quark-Antiquark Paar (Meson) oder als Kombination aus drei Quarks (Baryon) beobachtet. Mesonen und Baryonen werden unter dem Begriff Hadronen zusammengefaßt. Die starke Kernkraft beruht letztlich auf der Wechselwirkung zwischen Quarks, diese wird durch die Quantenchromodynamik (QCD) beschrieben. Ähnlich der Glashow- Salam-Weinberg Theorie (GSW), die die elektromagnetische und die schwache Kernkraft beschreibt, ist die Quantenchromodynamik durch Austauschteilchen charakterisiert. Im Fall der GSW wurden die Photonen bzw. W± oder Z-Teilchen als Austauschteilchen identifiziert, in der QCD fungieren Gluonen als Austauschteilchen. Photonen vermitteln die elektromagnetische Kraft zwischen allen Teilchen, die elektrische Ladung tragen. Analog wirkt die Kraft, die durch den Austausch von Gluonen beschrieben wird, zwischen Teilchen, die eine Farbladung tragen. Anders als das neutrale Photon trägt das Gluon selbst Farbe und wechselwirkt daher mit anderen Teilchen, die Farbe tragen. Dieser Umstand zeigt bereits, dass in der QCD ganz andere Phänomene zu erwarten sind als in der GSW. Die Tatsache, dass Quarks nur in gebundenen Zuständen vorliegen, erschwert die direkte Beobachtung der Wechselwirkung zwischen ihnen. Ein indirekter Weg, um die Wirkungweise diese Kraft zu untersuchen, liegt in der Erzeugung hoher Kernmateriedichten und hoher Kerntemperaturen. Die Idee besteht darin, das Phasendiagramm von Kernmaterie experimentell zu bestimmen (Abbildung 1.3) und dann auf die zugrundeliegende Kraft zu schließen. Unter anderem führen die Kräfte, die zwischen den Einzelteilchen des Mediums herrschen, zu charakteristischen Phasenübergängen. Im Fall der Kernmaterie hofft man insbesondere, den Übergang von gebundenen Zuständen in eine Quark-Gluon-Plasma Phase (QGP), in der sich Quarks und Gluonen frei bewegen, zu beobachten. Zwei prominente Beispiele demonstrieren, warum die Eigenschaften dieses Materiezustandes - und ob er überhaupt existiert - auch für andere Teilgebiete der Physik von großem Interesse sind. Zum einen geht man davon aus, dass in der Frühphase des Universums, 10-12 s nach dem Urknall, die Energiedichte so hoch war, dass die Materie in einem Plasmazustand vorlag. In diesem Bild führt die Expansion des Raumes zu einer Abkühlung des Plasmas und schließlich zum Ausfrieren in Hadronen. Zum anderen zeigen viele Modellstudien, dass im Innern von Neutronensternen mit extremen Dichten zu rechnen ist. Unter Umständen werden Energiedichten erreicht, die hoch genung sind, um einen Phasenübergang in ein Quark Gluon Plasma zu erzwingen. Die Beschreibung dieser astronomischen Objekte setzt somit auch die Kenntnis der Kräfte zwischen den Quarks voraus. Der einzige Weg, dichte Kernmaterie im Labor zu erzeugen, stellen Schwerionenreaktionen dar. Wenn zwei ultrarelativistische schwere Kerne zentral kollidieren, entsteht für kurze Zeit eine Region hoher Energiedichte (Abbildung 1.1). QCD-Gitter-Rechnungen deuten darauf hin, dass die Dichte, die man in Schwerionreaktion gegenwärtig erreicht, hoch genung ist, um einen Übergang der Kernmaterie in eine Plasma-Phase zu erzwingen. Aufgrund des hohen Drucks expandiert die verdichtete, heiße Kernmaterie in longitudinaler (entlang des Strahls) und transversaler (senkrecht zum Strahl) Richtung und die Dichte nimmt ab. Vorausgesetzt am Anfang der Reaktion wurde ein Quark-Gluon-Plasma erzeugt, dann friert diese Phase in Hadronen aus (chemisches Ausfrieren), wenn Dichte und Temperatur einen kritischen Wert unterschreiten. Die erzeugten Hadronen wechselwirken zunächst noch elastisch miteinander, d.h. die Impulse der Teilchen ändern sich, die Identität der Teilchen bleibt jedoch erhalten. Schließlich enden auch diese Wechselwirkungen (thermisches Ausfrieren), und die Teilchen verlassen die Reaktionszone (Abbildung 1.4). Der Ablauf einer solchen Schwerionenreaktion dauert einige 10-23s und ihre räumliche Ausdehnung liegt in der Größenordnung von 10-15m, damit ist die Reaktion selbst nicht beobachtbar. Nur der Endzustand, also die Identitäten und Impluse der emittierten Teilchen, kann bestimmt werden. Um den Ablauf der Reaktion zu rekonstruieren, ist man daher auf Modellrechnungen angewiesen. Aufgrund dieser Modellrechnungen wurden einige Observablen vorgeschlagen, die einen Phasenübergang kennzeichnen. Neben anderen Signaturen führt ein Phasenübergang wahrscheinlich zu einer verlängerten Emissionsdauer. Dieser Effekt kann möglicherweise durch die Analyse von Zwei-Teilchen-Korrelationen sichtbar gemacht werden. Ganz allgemein stellt die Untersuchung von Teilchenkorrelationen die einzige Möglichkeit dar, die raum-zeitlichen Strukturen während des thermischen Ausfrierens experimentell zu bestimmen. Korrelationen zwischen Teilchen, die von einer hinreichend kleinen Quelle emittiert werden, haben verschiedene Ursachen. Betrachtet man beispielsweise die Häufigkeitsverteilung der Impulsdifferenz zwischen zwei elektrisch gleich geladenen Teilchen, so stellt man fest, dass Paare mit geringer Impulsdifferenz weniger häufig vorkommen, als man anhand der Ein-Teilchen Impulsverteilung vorhersagen würde. Dieser Effekt ist auf die Abstoßung zwischen zwei elektrisch gleich geladenen Teilchen zurückzuführen, die mit kleiner Impulsdifferenz emittiert wurden. Eine weniger offensichtliche Korrelation wird durch den Quantencharakter identischer Teilchen verursacht. Zwei identische Bosonen, die im Phasenraum nahe beieinander liegen, können gemäß den Prinzipien der Quantentheorie nicht unterschieden werden. Die Wellenfunktion, die diesen Zwei-Teilchen-Zustand beschreibt, muß beim Vertauschen der Teilchen erhalten bleiben. Diese Forderung führt zu einem Interferenzterm in der Zwei-Teilchen Intensitätsverteilung. Diese Verteilung ist proportional zur Wahrscheinlichkeit, ein Teilchenpaar mit der Impulsdifferenz q zu messen. Berechnet man die Impulsdifferenzverteilung von Pionenpaaren und berücksichtig nur quanten- statistische Effekte, so findet man, dass Paare mit geringem Impulsunterschied bis zu zweimal häufiger vorkommen, als man aufgrund einfacher statistischer Überlegungen erwarten würde. Um diesen Effekt experimentell sichtbar zu machen, konstruiert man die Korrelationsfunktion, die die gemessene Impulsdifferenzverteilung in Relation zu einer Untergrundverteilung setzt. Experimentell gewinnt man diese Referenzverteilung, indem Paare aus Spuren aus verschiedenen Ereignissen gebildet werden. Die Referenzverteilung entspricht damit der Verteilung, die man messen würde, wenn die Teilchen nicht der Quantenstatistik unterlägen. Die Korrelationsfunktion wird im allgemeinen durch eine Gauß-Funktion angenähert. Das Inverse der Standardabweichung dieser Funktion wird nach den Pionieren der Intensitätsinterferometrie R. Hanbury Brown und R. Twiss als HBT-Radius bezeichnet. Teilchen interferieren nur dann, wenn sie im Phasenraum nahe beieinander liegen, das heißt sowohl die Impulsdifferenz als auch der räumliche Abstand muß hinreichend klein sein. Diese Bedingung kann genutzt werden, um von der gemessenen Korrelationsfunktion, die nur auf den Impulskomponenten basiert, auf die räumliche Verteilung der Teilchenproduktion zu schließen. Eine detaillierte Betrachtung erlaubt sogar, aufgrund der gemessenen Korrelationsfunktion quantitative Aussagen über die räumlichen Aspekte der Teilchenquelle zu machen. Beispielsweise können im Rahmen eines Modells die Stärke der transversalen Expansion oder die Emissionsdauer in Relation zu den HBT-Radien gesetzt werden. In Kapitel 2 sind die Grundlagen der Teilcheninterferometrie ausführlicher dargestellt. Der eigentliche Gegenstand dieser Arbeit ist experimentelle Analyse der Zwei- Teilchen-Korrelationen in einer Schwerionenreaktion. Dazu wird zunächst in Kapitel 3 das STAR Experiment am RHIC vorgestellt, in dem die Daten aufgezeichnet wurden, die Grundlage dieser Analyse sind. Am RHIC-Beschleuniger am BNL in den USA werden AuAu Kollisionen bis zu einer Schwerpunktsenergie von Wurzel aus SNN=200 GeV erzeugt. Figur 3.1 zeigt den Beschleuniger-Ring und die vier Experimente Brahms, Phenix, Phobos und STAR. Der hier analysierte Datensatz wurde bei der Datennahme im Jahr 2000 aufgezeichnet. Zu dieser Zeit wurde am RHIC eine Schwerpunktsenergie von Wurzel aus SNN=130 GeV erreicht. Bei einer zentralen AuAu Kollision werden mehrere Tausend Teilchen produziert. Der STAR Detektor ist dafür konzipiert, hadronische Teilchen kleiner Rapidität (d.h. großer Winkel zur Strahlachse) zu messen, innerhalb der Akzeptanz werden etwa 80% der produzierten geladenen Teilchen nachgewiesen. Der schematische Aufbau des STAR Detektorsystems ist in Figur 3.2 dargestellt. Der zentrale Detektor ist eine TPC (Zeit-Projektions-Kammer). Dieser Detektor basiert darauf, dass geladene Teilchen beim Durchgang durch ein Messgas eine Spur von Ionen hinterlassen. Ein starkes elektrisches Feld driftet die Elektronen, die bei den Ionisationsprozessen freigesetzt wurden, zu einer Ausleseebene. Der Punkt, an dem die Elektronen auf der Ausleseebene ein Signal erzeugen, entspricht der Projektion des Ionisationpunktes auf die Ausleseebene. Die dritte Komponente, die den Raumpunkt der Ionisation festlegt, ist durch die Driftzeit bei bekannter Driftgeschwindigkeit gegeben. So erscheint eine Teilchenspur als eine Kette von Ionisationspunkten im Detektorgas. Ein magnetisches Feld parallel zur Strahlachse führt zu einer Ablenkung der geladenen Teilchen. Die Krümmung der Spur ist dabei umgekehrt proportional zum transversalen Impuls. Abbildung 3.6 zeigt ein typisches Ereignis mit etwa 105 Ionisationspunkten und den entsprechenden Teilchenspuren. Der spezifische Energieverlust eines Teilchens beim Durchgang durch das Messgas hängt von seinem Impuls und seiner Masse ab. Die Stärke des auf der Ausleseebene induzierten Signals erlaubt den spezifischen Energieverlust zu bestimmen. Da der Impuls durch die Krümmung der Spur bekannt ist, kann so die Masse und damit die Identität des Teilchens bestimmt werden (siehe Abbildung 3.7). In Kapitel 4 wird der Datensatz beschrieben, der als Grundlage für diese Analyse dient. Während der Datennahme werden die digitalisierten Daten der TPC auf ein Speichermedium geschrieben. Der erste Schritt bei der Rekonstruktion der Ereignisse besteht darin, die Ionisationspunkte zu lokalisieren. Dies leistet der Clusterfinder- Algorithmus, der in Kapitel 4.1.1 beschrieben ist. Die Spurpunkte werden dann durch den Tracking-Algorithmus zu Teilchenspuren verbunden. Die erreichte Effizienz, Akzeptanz und Impulsauflösung der Rekonstruktion sind in Kapitel 4.1.2 zusammengefaßt. Die Zwei-Teilchen-Korrelationen werden nur für zentrale Kollisionen betrachtet, das sind Ereignisse mit kleinem Stoßparameter. Die Multipliztät der gemessenen Spuren ist in erster Näherung ein Maß für die Zentralität des Ereignisses. Für diese Analyse werden nur die 12% zentralsten Ereignisse zugelassen. Die Selektion der Ereignisse ist in Kapitel 4.2 beschrieben. Die Auswahl der Spuren, die in der Analyse verwendet werden, ist in Kapitel 4.3 beschrieben. Es werden nur Spuren zugelassen, deren Impulse in einem Bereich hinreichend hoher Akzeptanz und Effizienz liegen. Außerdem werden die Spuren ausgewählt, die mit hoher Wahrscheinlichkeit von Pionen stammen. Eine weitere Auswahl wird auf der Paarebene getroffen. Die Korrelationsfunktion wird in einzelnen Intervallen transversalen Paarimpulses kt und Paarrapidität Yðð gebildet. Damit kann die Abhängigkeit der HBT-Radien von diesen Größen dargestellt werden. Zwei weitere Auswahlkriterien sollen die Qualität der Spurpaare garantieren. Zum einen werden solche Paare verworfen, die im Detektor zu nahe beieinander liegen. Für die HBT-Analyse sind Paare mit geringem Impulsunterschied entscheidend, ein geringer Impulsunterschied heißt notwendigerweise, dass die Spuren räumlich nicht sehr weit getrennt sind. Wenn die Spuren aber zu nahe liegen, können sie vom Detektor und von der Rekonstruktionskette nicht mehr aufgelöst werden. Damit verliert man einen Teil der Paare in der Signalverteilung, nicht aber in der Untergrundverteilung, da in diesem Fall die endliche Zwei-Spur-Auflösung keine Rolle spielt. Um die Korrelationsfunktion nicht durch einen Detektoreffekt zu verfälschen, entfernt man die Paare, die im Detektor nahe beieinander liegen, sowohl in der Signal- als auch in der Untergrundverteilung. Ein weiteres Problem stellen "gebrochene" Spuren dar. In einigen Fällen wird eine Teilchenspur von der Rekonstruktionskette nicht als Ganzes erkannt, vielmehr werden zwei Spurstücke im Dektor gefunden. Da diese Spurstücke vom selben Teilchen stammen, haben sie eine sehr geringe Impulsdifferenz. Diese Paare können anhand ihrer Topologie im Detekor erkannt werden. Wie im Fall der begrenzten Zwei-Spur-Auflösung werden sie sowohl für die Signal- als auch für die Untergrundverteilung nicht zugelassen. In Kapitel 5 werden schließlich die Ergebnisse der Korrelationsanalyse dargestellt. Die Korrelationsfunktion wird in verschiedenen Parametrisierungen betrachtet. In der einfachsten Form betrachtet man nur den Betrag des Impulsdifferenzvektors. Dieser Ansatz bedeutet aber, dass der entsprechende HBT-Radius alle Raum-Zeit Komponenten mischt und damit nur wenig Aussagekraft bezüglich der Quellfunktion besitzt. Eine differenzierte Analyse in drei unabhängigen Komponenten ermöglichen die Pratt-Bertsch (PB) und die Yano-Koonin-Podgoretskii (YKP) Parametrisierung. Die beiden Parametrisierungen unterscheiden sich in der Zerlegung des Impulsdifferenzvektors in drei unabhängige Komponenten. Im ersten Fall bezeichnet man die Komponenten als qout, qlong und qside, im zweiten Fall als qpara, qperp und q0 (Kapitel 2.7 und 2.8). Die entsprechenden Korrelationsfunktionen sind in Gleichung 2.31 bzw. 2.34 gegeben. Die jeweiligen HBT-Radien Rout, Rlong und Rside bzw. Rpara, Rperp und R0 können in Relation zu den Parametern der Quellfunktion (Gleichung 2.43) gesetzt werden. Die beiden Parametrisierungen liefern im Prinzip die gleiche Information und die beiden Sätze von HBT-Radien können in Beziehung zueinander gesetzt werden (Gleichung 2.41). Beispielsweise entspricht der HBT-Radius R0 in der YKP-Parametrisierung in erster Näherung der Emissionsdauer, während in der PB- Parametrisierung diese Größe Verhältnis von Rout zu Rside abhängt. Zusätzlich zu den Radien enthält die YKP-Parametrisierung einen Parameter ß, der erlaubt, die longitudinale Geschwindigkeit des betrachteten Quellelementes zu bestimmen. Die Abbildungen 5.7 bis 5.10 zeigen die HBT-Radien beider Parametrisierungen in Abhänigigkeit vom transversalen Paarimpuls kt und von der Paarrapidität Yðð. Die Größe der gemessenen Radien bewegt sich zwischen 3 und 7 fm. Nur der Radius R0 verschwindet in den meisten kt-Yðð Intervallen. Die anderen Radien nehmen mit steigendem kt ab und sind unabhängig von Yðð . Abbildung 5.11 demonstriert, dass die beiden Parametrisierungen -dort wo sie vergleichbar sind- konsistente Ergebnisse liefern. Eine Diskussion der Ergebnisse schließt sich in Kapitel 6 an. Die Abhänigigkeit des Parameters ß von Yðð zeigt eine starke longitudinale Expansion an. Ein ähnliches Verhalten wurde bei niedrigeren Schwerpunktsenergien beobachtet, wo man allerdings eine schwächere longitudinale Expansion erwarten würde. Die Lebensdauer der Quelle, also die Zeit vom anfänglichen Überlapp der Kerne bis zum thermischen Ausfrieren, bestimmt die kt-Abhänigigkeit des Parameters Rlong. Dieser Zusammenhang wurde von Mahklin und Sinyukow formuliert, eine Anpassung der entsprechenden Funktion an die gemessene kt Abhänigigkeit von Rlong ergibt eine Lebensdauer von etwa 8 fm/c bei einer Ausfriertemperatur von etwa 126 MeV. Entsprechende Messungen bei niedrigeren Kollisionsenergien lieferten ähnliche Resultate. Die kt-Abhängigkeit des Parameters Rside ist mit der Stärke der transversalen Expansion gemäß Gleichung 6.3 verknüpft. Da die Relation nicht eindeutig ist, muß entweder eine feste Ausfriertemperatur angenommen werden oder es werden gleichzeitig Einteilchenspektren betrachtet, um die Mehrdeutigkeit zu eliminieren. Eine vorläufige Abschätzung ergibt eine mittlere transversale Expansions- geschwindigkteit von v ungefähr gleich 0.6 und einen gemetrischen Radius von RG ungefähr gleich 7.4 fm . Auch diese Ergebnisse sind vergleichbar mit entsprechenden Resultaten bei niedrigeren Kollisionsenergien. Ein weiterer Parameter der Quellfunktion ist die Emissionsdauer. Die Pionen werden nicht zu einem festen Zeitpunkt emittiert, man geht vielmehr davon aus, dass die Zeitpunkte der letzten elastischen Wechselwirkung in der Quelle gaußförmig verteilt sind. Den Mittelwert dieser Verteilung bezeichnet man als Lebensdauer der Quelle, die Breite als Emissionsdauer. Entsprechend Gleichung 6.4 bzw. 6.5 ist die Emissionsdauer mit dem Radius R0 bzw. dem Verhältnis Rout zu Rside verbunden. Wie in Abbildung 5.8 ersichtlich verschwindet der Parameter R0 , außer im kleinsten kt Intervall. Dies entspricht in der PB-Parametrisierung der Tatsache, dass das Verhältnis Rout zu Rside bei hohen kt kleiner als eins ist. Diese Resultate sind nicht vereinbar mit herkömmlichen Modellen. Insbesondere weil eine verlängerte Emissionsdauer als Signatur für die Bildung eines Quark-Gluon-Plasmas vorgeschlagen wurde, wird dieses Ergebnis derzeit intensiv diskutiert. Die Ergebnisse dieser Analyse sind sowohl mit bereits publizierten Daten der STAR Kollaboration als auch mit Resultaten von anderen RHIC Experimenten verträglich (siehe Abbildung 6.8). In Abbildung 6.9 ist die Abhängigkeit der HBT-Radien von kt bei verschiedenen Schwerpunktsenergien dargestellt. Im Gegensatz zu vielen anderen Observablen ändern sich die HBT Radien nur geringfügig. Da man erwartet, dass die Reaktion bei hohen Energien vollkommen anders abläuft, würde man auch davon ausgehen, dass sich die Ausfrierbedingungen ändern. Dass dies nicht in den Zwei-Teilchen- Korrelationen sichtbar wird, deutet darauf hin, dass die Näherungen die notwendig sind, um die gemessenen Radien mit Modellparametern zu verbinden, nicht gültig sind. Die Systematik der HBT Parameter als Funktion der Schwerpunktsenergie enthält damit keinen direkten Hinweis, dass die kritische Energiedichte überschritten wurde, ab der die Kernmaterie in einer Plasmaphase vorliegt. Andererseits werden weder die verschwindende Emissionsdauer noch die Tatsache, dass die anderen HBT-Parameter sich nur wenig mit der Schwerpunktsenergie ändern, als Argument dafür gewertet, dass die kritische Energiedichte nicht überschritten wurde. Die Frage, ob ein Quark- Gluon-Plasma im Labor erzeugt und analysiert werden kann, bleibt damit offen. Das thermische Ausfrieren einer Pionenquelle scheint hingegen anders zu verlaufen, als bisher angenommen wurde. Systematische Studien der Korrelationsfunktion in AA Kollisionen am RHIC in Kombination mit Fortschritten im theoretischen Verständnis der Teilcheninterferometrie in Schwerionenreaktion werden in Zukunft hoffentlich erlauben, die gemessenen Radien in ein konsistentes Bild einzuordnen. In zukünftigen Experimenten am LHC werden noch weit höhere Dichten erreicht als bisher, damit sollten sich auch die Ausfrierbedingungen stark verändern. Es wird sich dann zeigen, ob die Teilcheninterferometrie das geeignete Instrument ist, um die Quellfunktion einer Schwerionenreaktion zu messen.
Die Arbeit beschäftigt sich mit der Herstellung sowie der strukturellen und magnetischen Charakterisierung von zwei Materialklassen von kupferbasierten zweidimensionalen Quanten-Spin-Systemen: Quadratische Gitter von Dimeren sowie geometrisch frustrierte Kagomé Gitter. In beiden Systemen werden Substitutionen vorgestellt die zu verbesserten Eigenschaften führen.
Tuning and optimization of the field distribution for 4-rod radio frequency quadrupole linacs
(2014)
In this thesis, the tuning process of the 4-rod Radio Frequency Quadrupole has been analyzed and a theory for the prediction of the tuning plate's influence on the longitudinal voltage distribution was developed together with RF design options for the optimization of the fringe fields.
The basic principles of the RFQ's particle dynamics and resonant behavior are introduced in the theory part of this thesis. All studies that are presented are based on the work on four RFQs of recent linac projects. These RFQs are described in one chapter. Here, the projects are introduced together with details about the RFQ parameters and performance. In the meantime two of these RFQs are in full operation at NSCL at MSU and FNAL. One is operating in the test phase of the MedAustron Cancer Therapy Center and the fourth one for LANL is about to be built. The longitudinal voltage distribution has been studied in detail with a focus on the influence of the RF design with tuning elements and parameters like the electrodes overlap or the distance between stems. The theory for simulation methods for the field flatness that were developed as part of this thesis, as well as its simulation with CST MWS have been analyzed and compared to measurements. The lumped circuit model has proven to predict results with an accuracy that can be used in the tuning process of 4-rod RFQs. Together with results from the tuning studies, the studies on the fringe fields of the 4-rod structure lead to a proposal for a 4-rod RFQ model with an improved field distribution in the transverse and longitudinal electric field.
Solute carrier (SLC) are related to various diseases in human and promising pharmaceutical targets but more structural and functional information on SLCs is required to expand their use for drug design and therapy. The 7-transmembrane segment inverted (7-TMIR) fold was identified for the SLC families 4, 23 and 26 in the last decade thus detailed analysis of the structure function relationship of one of these families might also yield insights for the other two. SVCT1 and SVCT2 from the SLC23 family are sodium dependent ascorbic acid transporters in human but structural analysis of the SLC23 family is exclusively based on two homologs – UraA from E. coli and UapA from A. nidulans – yielding two inward-facing and one occluded conformation. In combination with outward-facing conformations from SLC4 transporters, and additional information from the SLC26 family, an elevator transport mechanism for all 7-TMIR proteins was identified but detailed mechanistic features of the transport remain elusive due to the lack of multiple conformations from individual transporters.
To increase the understanding of 7-TMIR protein structure and function in this study, the transport mechanism of SLC23 transporters was analyzed by two strategies including selection of alpaca derived nanobodies and synthetic nanobodies against UraA as prokaryotic model protein of the SLC23 family. The second strategy involved mutagenesis of UraA at functional relevant positions regarding the conformational change during transport. Therefore, available structures of 7-TMIR proteins and less related elevator transporters were analyzed and a common motif identified – the alpha helical inter-domain linkers. The proposed rigid body movement for transport in combination with the characteristic alpha helical secondary structure of the linkers connecting both rigid bodies led to the hypothesis of functional relevance of the linkers and a conformational hinge being located in close proximity to the linkers. These positions were identified and used to modulate the biophysical properties of the transporter. Mutagenesis at three relevant positions led to loss of transport functionality and these UraA variants could be recombinantly produced and purified to further examine the underlying mechanistic effects. The variants UraAG320P and UraAP330G from the periplasmic inter-domain linker showed increased dimerization and thermal stability as well as substrate binding in solution. The substrate affinity of UraAG320P was identified to be 5-fold higher compared to the wildtype. The solvent accessibility of the substrate binding site in UraAG320P and UraAP330G revealed reduced open probability that indicated an altered conformational space compared to UraAWT. This phenomenon was analyzed in more detail by differential hydrogen-deuterium exchange mass spectrometry and the results supported the hypothesis of a reduced open probability and gave further insights into the impact of the two mutations in the periplasmic inter-domain linker in UraA.
This thesis further presents strategies for phage display selection of nanobodies with epitope bias and a post selection analysis pipeline to identify nanobodies with desired binding characteristics. Thereby, whole cell transport inhibition highlighted periplasmic epitope binders and conformational selectivity. A cytoplasmic epitope could be identified by pulldown with inside-out membrane vesicles for one cytoplasmic side binder. Thermal stabilization analysis of the target protein in differential scanning fluorometry was performed in presence of two different nanobodies to identify simultaneous binding by additional thermal stabilization respectively competition by intermediate melting temperatures. Combination of epitope information with simultaneous DSF could be used to identify the stabilization of different UraA conformations by a set of binders and presents a general nanobody selection strategy for other SLCs. Synthetic nanobodies (sybodies) were also included in the analysis pipeline and Sy45 identified as promising candidate for co-crystallization that gave rise to UraAWT crystals in several conditions in presence or absence of uracil. Similar crystals could be obtained in combination with UraAG320P that were further optimized to gain structural information on this mutant. The structure was solved by molecular replacement and the model refined at 3.1 Å resolution confirming the cytoplasmic epitope of Sy45 as predicted by the selection pipeline. The stabilized conformation was inward-facing similar to the reported UapA structure but significantly different to the previously reported inward-facing structure of UraA. The structure further confirmed the structural integrity of the UraA mutant G320P. Despite the monomeric state of UraA in the structure, the gate domain aligned reasonably well with the gate domain of the previously published dimeric UraA structure in the occluded conformation and allowed detailed analysis of the conformational transition in UraA from inward-facing to occluded by a single rigid body movement. Thereby little movement in the gate domain of UraA was observed in contrast to a previously reported transport mechanism. Core domain rotation around a rotation axis parallel to the substrate barrier was found to explain the major part of conformational transition from inward-facing to occluded and experimentally supported the hypothesized mechanism by Chang et al. (2017). Additionally, the conformational hinge around position G320 in UraA could be identified as well as the impact of the backbone rigidity introduced by the highly conserved proline residue at position 330 in UraA on the conformational transition. This position was found to serve as anchoring point the inter-domain linker and determines the coordinated movement of inter-domain linker and core domain. The functional analysis further highlighted the requirement of alpha helical secondary structure within the inter-domain linker that serves as amphipathic structural entity that can adjust to changed core-gate domain distances and angles during transport by extension/compression or bending while preserving the rigid linkage.
The applied strategies to modulate the conformational space of UraA by mutagenesis at the hinge positions in the inter-domain linkers is transferrable to other transporters and might facilitate their structural and functional characterization.
Further, this study discusses the conformational thermostabilization of UraA that is based on increased melting temperatures upon restriction of its conformational freedom. The term ‘conformational thermostabilization’ introduced by Serrano-Vega et al. (2007) could be experimentally supported and the direct correlation between the conformational freedom and thermostabilization was qualitatively analyzed for UraA. The concept of conformational thermostabilization might help in characterization of other dynamic transport systems as well.
Tulasnella species (Tulasnellaceae, Cantharellales, Basidiomycota) form inconspicuous basidiomata on rotten branches or trunks of trees, difficult to find and recognize in nature. However, according to ultrastrucural and molecular data, species of Tulasnellaceae are the most frequent mycorrhriza forming fungi (mycobionts) of green, photosynthetic orchids worldwide. Species of Tulasnellaceae were also found as prominent mycobionts of the extraordinary diverse orchids in tropical montane rainforest of Southern Ecuador. Orchids obligately depend on mycobionts during the juvenile stage when the fungi have to deliver carbon to the non-photosynthetic protocorm and thus the fungi substantially influence the establishment of orchids in the wild. Species of Tulasnellaceae can acquire carbon from decaying bark or wood by specific saprotrophic capabilities as was recently proven through comparative genomics that included data on decay enzymes from Tulasnella cf. calospora isolated from orchid mycorrhizae (Anacamptis laxiflora, Italy). Thus, species of Tulasnellaceae can be saprotrophs and symbionts simultaneously.
It is currently under discussion, whether specific species of Tulasnella are required for seed germination and establishment of distinct terrestrial and epiphytic orchids in nature or if species of Tulasnella are generalists concerning their association with orchids. The inconsistences in species concepts and taxonomy of Tulasnella spp., however, strongly impede progress in this field of research. The aim of the present study was, therefore, to revise the species concepts by combining, for the first time, morphological and molecular data from basidiomata.
Specimens were collected in tropical Andean forest in Southern Ecuador and in temperate forests in Germany. Additional specimens were loaned from fungaria. In total, 205 specimens, corresponding to 16 own samples and 189 specimens from fungaria were analyzed. The mycobiont relationships of Tulasnella spp. with orchids from the sampling area in Ecuador were studied in populations of Epidendrum rhopalostele. The basis for molecular-phylogenetic analysis was completed by data obtained from own previous investigations on mycobionts from the investigation area and Tulasnella isolates from Australia.
30 morphospecies are illustrated and delimited by a morphological key based on traditional species concepts. Tulasnella andina from Ecuador and Tulasnella kirschneri from China are presented as species new to science. Tulasnella cruciata is described from herbarium material for the first time. Tulasnella aff. eichleriana and T. violea are reported for the first time from Ecuador. Molecular sequences of two Tulasnella spp. isolated from mycobionts of Epidendrum rhopalostele cannot be related to any morphological species concept. Statistical analyses suggest that conventional diagnostic using morphological characteristics is ambiguous for delimiting morphologically similar species.
For the first time sequences of the ITS-5.8S rDNA region were obtained after cloning from fresh basidiomata. Extraction of DNA from herbarium specimens was, however, unsuccessful. Sequences from 16 fresh basidiomata, six pure cultures, and sequences of orchids mycorrhizae (e.g. from Epidendrum rhopalostele) available in the database GenBank were analyzed. Proportional
variability of ITS-5.8S rDNA sequences within and among cultures and within and among specimens were used to designate morphospecies. Results suggest an intragenomic variation of less than 2 %, an intraspecific variation of up to 4 % and an interspecific divergence of more than 9 % for Tulasnella spp.
Four percent of intraspecific divergence was defined as a minimum threshold for delimiting phylogenetic species. This threshold corroborates the so far used 3 % to 5 % divergence in delimitation of operational taxonomic units of Tulasnella mycobionts.
Quite a number of sequences of Tulasnella are available in GenBank, mostly obtained from direct PCR amplification from orchid mycorrhizae. By including closely related sequences in the phylogenetic analysis, several morphological cryptic species of Tulasnella, mostly from Ecuador, were found. Arguments are given for molecular support of the new species Tulasnella andina and the established species Tulasnella albida, T. asymmetrica, T. eichleriana, T. tomaculum, and T. violea. Thus, by combining molecular and morphological data species concepts in Tulasnella are improved. The definitions of Tulasnella calospora and T. deliquescens, however, remain phylogenetically inconsistent.
The present investigation is a first step to expand our knowledge on the intraand interspecific morphological and molecular variability of Tulasnella spp. and to delimit species relevant for studies on ecology and communities of orchids and Tulasnellaceae.
Organische Materialien haben bis zur Mitte des 20. Jahrhunderts hinsichtlich ihrer elektronischen Eigenschaften keine besondere Aufmerksamkeit auf sich gezogen. Größeres Interesse an diesen Materialien entstand erst durch die Entdeckung einer ungewöhnlich hohen elektrischen Leitfähigkeit des organischen Perylen-Bromin Ladungstransfer-Komplexes durch Inokuchi et al. im Jahr 1954. Diese neue Klasse von Materialien besteht typischerweise aus Donor- und Akzeptor-Molekülen, die in einer bestimmten Stöchiometrie aneinander gebunden sind. Elektrische Ladung wird zwischen den Donor- und Akzeptor-Molekülen transferiert. Um diesen Prozess zu beschreiben, entwickelte Robert Mulliken in den 60er Jahren ein theoretisches Gerüst. Abhängig von der Anordnung der Moleküle und transferierten elektrischen Ladung kann der Ladungstransfer-Komplex (oder Salz) ein Isolator, ein Halbleiter, ein Metall oder sogar ein Supraleiter sein. Noch mehr Aufmerksamkeit erhielten Ladungstransfer-Materialien mit der Entdeckung des ersten quasi-eindimensionalen organischen Metalls TTF-TCNQ (tetrathiafulvalene-tetracyanoquinodimethane) im Jahr 1973. ...
Protein quality control (PQC) machinery is in charge of ensuring protein homeostasis in the cell, i.e. proteostasis. Chaperones assist polypeptides throughout their maturation until functionality is achieved. This process might be disrupted in the presence of mutations or external damaging agents that affect the folding and stability of proteins. In this case, proteins can be efficiently recognized and targeted for degradation in a controlled manner. Ubiquitylation refers to the covalent attachment of one or more ubiquitin moieties to faulty proteins, thus triggering their degradation by the 26S proteasome.
More than 30% of proteins need cofactor molecules. Lack of cofactors renders proteins non-functional. We wanted to understand how the PQC deals with wild-type proteins in the absence of their cofactors. Several studies have indicated the importance of the riboflavin-derived cofactor FAD in the stability of individual flavoproteins, and hence we assumed that loss of flavin should mediate a targeted degradation of this group of proteins. Indeed, our mass spectrometry experiments showed that flavoproteome levels decreased under riboflavin starvation. The oxidoreductase NQO1 was used as a model enzyme to further investigate the mechanism of flavoproteome targeting by the PQC. We showed that cofactor loading determines ubiquitylation of NQO1 by the co-chaperone CHIP, both in vivo and in vitro. Furthermore, subtle changes in the C-terminus of NQO1 in the absence of FAD seemed to be crucial for this recognition event. ApoNQO1 interactome differed from holoNQO1. Chaperones and degradation factors were enriched on NQO1 upon cofactor withdrawal, probably to support maturation and prevent aggregation of the enzyme.
Loss of protein folding and stability, even to a small extent, can enhance the aggregating behavior of proteins. Proper loading with FAD reduced the co-aggregation of NQO1 with Aβ1-42 peptide. We assumed that the flavoproteome might represent aggregating-prone species under riboflavin deprivation. Supportingly, reversible apoNQO1 aggregates were observed in vivo in the absence of cofactor. General amyloidogenesis in vivo also increased under these conditions, apparently as a result of flavoproteome destabilization. In this context, we think that our data might have important implications considering the onset and development of conformational diseases.
This work has shed some light on the therapeutic implications of riboflavin deficiency as well. The sensitivity of melanoma cells towards the alkylating agent methyl methanesulfonate (MMS) increased under riboflavin starvation. Subsequent analyses indicated that a complex metabolic reorganization, mostly affecting proliferation and energy metabolism, occurs in response to starvation. What we suggest to call “flavoaddiction” can be understood as the dependence of melanoma cells on the flavoproteome structural and functional intactness to survive chemotherapy. Understanding this cellular reprogramming in detail might reveal new possibilities for future therapies.
Manual development of deep linguistic resources is time-consuming and costly and therefore often described as a bottleneck for traditional rule-based NLP. In my PhD thesis I present a treebank-based method for the automatic acquisition of LFG resources for German. The method automatically creates deep and rich linguistic presentations from labelled data (treebanks) and can be applied to large data sets. My research is based on and substantially extends previous work on automatically acquiring wide-coverage, deep, constraint-based grammatical resources from the English Penn-II treebank (Cahill et al.,2002; Burke et al., 2004; Cahill, 2004). Best results for English show a dependency f-score of 82.73% (Cahill et al., 2008) against the PARC 700 dependency bank, outperforming the best hand-crafted grammar of Kaplan et al. (2004). Preliminary work has been carried out to test the approach on languages other than English, providing proof of concept for the applicability of the method (Cahill et al., 2003; Cahill, 2004; Cahill et al., 2005). While first results have been promising, a number of important research questions have been raised. The original approach presented first in Cahill et al. (2002) is strongly tailored to English and the datastructures provided by the Penn-II treebank (Marcus et al., 1993). English is configurational and rather poor in inflectional forms. German, by contrast, features semi-free word order and a much richer morphology. Furthermore, treebanks for German differ considerably from the Penn-II treebank as regards data structures and encoding schemes underlying the grammar acquisition task. In my thesis I examine the impact of language-specific properties of German as well as linguistically motivated treebank design decisions on PCFG parsing and LFG grammar acquisition. I present experiments investigating the influence of treebank design on PCFG parsing and show which type of representations are useful for the PCFG and LFG grammar acquisition tasks. Furthermore, I present a novel approach to cross-treebank comparison, measuring the effect of controlled error insertion on treebank trees and parser output from different treebanks. I complement the cross-treebank comparison by providing a human evaluation using TePaCoC, a new testsuite for testing parser performance on complex grammatical constructions. Manual evaluation on TePaCoC data provides new insights on the impact of flat vs. hierarchical annotation schemes on data-driven parsing. I present treebank-based LFG acquisition methodologies for two German treebanks. An extensive evaluation along different dimensions complements the investigation and provides valuable insights for the future development of treebanks.
We study exchangeable coalescent trees and the evolving genealogical trees in models for neutral haploid populations.
We show that every exchangeable infinite coalescent tree can be obtained as the genealogical tree of iid samples from a random marked metric measure space when the marks are added to the metric distances. We apply this representation to generalize the tree-valued Fleming-Viot process to include the case with dust in which the genealogical trees have isolated leaves.
Using the Donnelly-Kurtz lookdown approach, we describe all individuals ever alive in the population model by a random complete and separable metric space, the lookdown space, which we endow with a family of sampling measures. This yields a pathwise construction of tree-valued Fleming-Viot processes. In the case of coming down from infinity, we also read off a process whose state space is endowed with the Gromov-Hausdorff-Prohorov topology. This process has additional jumps at the extinction times of parts of the population.
In the case with only binary reproduction events, we construct the lookdown space also from the Aldous continuum random tree by removing the root and the highest leaf, and by deforming the metric in a way that corresponds to the time change that relates the Fleming-Viot process with a Dawson-Watanabe process. The sampling measures on the lookdown space are then image measures of the normalized local time measures.
We also show invariance principles for Markov chains that describe the evolving genealogy in Cannings models. For such Markov chains with values in the space of distance matrix distributions, we show convergence to tree-valued Fleming-Viot processes under the conditions of Möhle and Sagitov for the convergence of the genealogy at a fixed time to a coalescent with simultaneous multiple mergers. For the convergence of Markov chains with values in the space of marked metric measure spaces, an additional assumption is needed in the case with dust.
Flexibility and constraints in migration and breeding of the barnacle goose Maximising fitness means, to a large extent, optimising management of time and energy. This thesis investigates aspects of timing and resource acquisition and utilisation in the barnacle goose Branta leucopsis during spring migration and reproduction. The barnacle goose population wintering along the Wadden Sea coast, and traditionally migrating via a stopover in the Baltic to its breeding sites in northern Russia, has shown some remarkable developments, among them, a geometric growth rate since the 1950s and a notable change in the timing of departure from the wintering grounds. Furthermore, long being regarded as an obligate Arctic breeder, within the past three decades this species has successfully colonised a wide variety of habitats at temperate latitudes, thereby shortening the migratory distances considerably or refraining from migration altogether. These remarkable changes raise questions about the flexibility of migratory and reproductive schedules. What are the costs and benefits of different migration strategies? And, given the context of global change, to what extent are animals capable of adapting to rapidly changing environments? In order to answer these questions we tracked migratory geese by satellite and with the help of data loggers and, furthermore, explored possible relationships of migratory behaviour and breeding performance. Another central thesis topic represents a within-species comparison of major life-history traits in populations breeding along a large ecological gradient from arctic to temperate environments. Fieldwork was conducted in arctic Russia, Sweden and The Netherlands.
Informally, commitment schemes can be described by lockable steely boxes. In the commitment phase, the sender puts a message into the box, locks the box and hands it over to the receiver. On one hand, the receiver does not learn anything about the message. On the other hand, the sender cannot change the message in the box anymore. In the decommitment phase the sender gives the receiver the key, and the receiver then opens the box and retrieves the message. One application of such schemes are digital auctions where each participant places his secret bid into a box and submits it to the auctioneer. In this thesis we investigate trapdoor commitment schemes. Following the abstract viewpoint of lockable boxes, a trapdoor commitment is a box with a tiny secret door. If someone knows the secret door, then this person is still able to change the committed message in the box, even after the commitment phase. Such trapdoors turn out to be very useful for the design of secure cryptographic protocols involving commitment schemes. In the first part of the thesis, we formally introduce trapdoor commitments and extend the notion to identity-based trapdoors, where trapdoors can only be used in connection with certain identities. We then recall the most popular constructions of ordinary trapdoor protocols and present new solutions for identity-based trapdoors. In the second part of the thesis, we show the usefulness of trapdoors in commitment schemes. Deploying trapdoors we construct efficient non-malleable commitment schemes which basically guarantee indepency of commitments. Furthermore, applying (identity-based) trapdoor commitments we secure well-known identification protocols against a new kind of attack. And finally, by means of trapdoors, we show how to construct composable commitment schemes that can be securely executed as subprotocols within complex protocols.
Transylvanian Saxons' migration from Romania to Germany: the formation of a 'return' diaspora?
(2013)
Processes and patterns of migration on a global scale have changed in profound ways during the last two decades (Smith and King, 2012). In the European context, this is exemplified by transformations to the traditional mobility patterns from East to West Europe (Koser and Lutz, 1998), with migrants more likely to be involved in temporary circular and transnational mobility (Favell, 2008). Since the end of the Second World War, historical and political events in Europe have facilitated the mobility of ethnic Germans from Eastern Europe to Germany. Subsequently, the fall of the Iron Curtain has permitted unrestrained East-West movements, which resulted in mass migrations towards the West and diaspora fragments in the East. However, after settlement in the West, ethnic Germans have also been absorbed within wider temporary and transnational movements (Koser, 2007). Within this context, this thesis examines the post-migratory lives of three generations of Transylvanian Saxons in Germany by exploring the cultural, social, economic and political dimensions of this community. This thesis aims to contribute to on-going academic debates about diasporas by explicitly responding to Hoerder s (2002) call for more studies on ethnic German diasporas. It shows that Transylvanian Saxons, who relocated to the ancestral homeland, do not disrupt identities and lives forged in diaspora, but rather, they negotiate complex identities and belongings in relation to both home and homeland . It reveals a double diaspora and the necessity to perceive identity and diaspora as dynamic processes and constantly evolving in relation to time, space and place. This double diasporic allegiance in the case of the Transylvanian Saxons suggests interrogating the formation of a return diaspora and its importance for processes of international migration.
The production cross section and the transverse momentum distribution of charged particles is measured in pp collisions at √s = 2.76 TeV, 5.02 TeV, 7 TeV and 13 TeV, as well as for Pb-Pb collision at √s_NN = 5.02 TeV and Xe-Xe at √s_NN = 5.44 TeV in ALICE at the LHC. The measurement is performed in the transverse momentum region of 0.15 < p_T < 50 GeV/c and in the pseudorapidity range of |η| < 0.8. The precision of the measurement has been substantially enhanced as a result of the improved corrections, by taking into account a more realistic particle composition in the MC simulations. As a result, the systematic uncertainties have been reduced by more than a factor two in all systems and energies.
The average transverse momentum <p_T> results show a faster-than-linear increase with the center-of-mass energy and follow a similar trend with respect to previous measurements. The analysis of the p_T spectra in multiplicity intervals show a weak center-of-mass energy dependence when they are compared to their respective inelastic (INEL) pp measurement. The average multiplicity as a function of the collision energy shows a quadratic trend, and the comparison with other ALICE multiplicity measurements exhibits a remarkable agreement, within uncertainties.
The transverse momentum spectra in pp collisions are compared to state-of-the-art MC simulations, EPOS LHC and PYTHIA 8 event generators; none of them is able to reproduce the distributions over the full p_T range.
The differential cross section in pp collisions is an essential observable for the study of the Quark Gluon Plasma (QGP) created in ultra-relativistic heavy-ion collisions. The absence of a medium formation in pp collisions serves as an essential baseline for studies of particle production and suppression due to parton energy-loss in the QGP. Since pp collisions at √s = 5.44 TeV were not measured by ALICE, the pp reference at this energy was constructed by using a power law interpolation between the s = 5.02 TeV and 7 TeV data. The pp results are compared to the particle production in Pb-Pb collisions at √s_NN = 5.02 TeV and Xe-Xe collisions at √s_NN = 5.44 TeV.
The nuclear modification factor R_AA for Pb-Pb and Xe-Xe collisions was calculated and a strong suppression of high-p_T particles is observed in central collisions. The R AA in different systems allows for a differential study of the parton energy loss in the QGP. The comparison of the R AA in multiplicity intervals between the two systems provide insights into the path length dependence of a parton that propagates in the medium.
Ziel dieser Dissertation ist es, die Gleichgewichts- und Nichtgleichgewichts-Eigenschaften des stark wechselwirkenden QGP-Mediums nahe dem Phasenübergang unter extremen Bedingungen von hohen T und hohen Baryonendichten mit Hilfe der kinetischen Theorie im Rahmen von effektiven Modellen zu untersuchen. Wir werden zunächst die thermodynamischen und Transporteigenschaften des QGPs in der Nähe des Gleichgewichts auf der Basis des DQPM im Bereich moderater chemischer Baryonenpotentiale μB ≥ 0.5 GeV untersuchen. Insbesondere werden die EoS und die Schallgeschwindigkeit sowie die Transportkoeffizienten des QGP auf der Grundlage des DQPM bei endlichen T und μB berechnet. Transportkoeffizienten sind besonders interessant, da sie Informationen über die Wechselwirkungen im Medium erlauben, das im Gleichgewicht durch eine Temperatur T und ein chemisches Potential μB charakterisiert werden kann. Unter Berücksichtigung der Transportkoeffizienten und der EoS der QGP-Phase vergleichen wir unsere Ergebnisse mit verschiedenen Resultaten aus der Literatur, in denen Transportkoeffizienten des QGPs auf Basis von effektiven Modellen vorwiegend bei Null oder kleinem chemischen Potentialen untersucht wurden.
Darüber hinaus werden in Kapitel 3 die Gleichgewichtseigenschaften des QGPs und insbesondere die Auswirkungen der μB-Abhängigkeit der thermodynamischen und Transporteigenschaften des QGPs im Rahmen des erweiterten PHSD-Transportansatzes untersucht, der die vollständige Entwicklung des Systems einschließlich der partonischen Phase umfasst. Die Entwicklung des PHSD-Transportansatzes wird in der partonischen Phase erweitert, indem explizit die gesamt- und differentiellen partonischen Streuquerschnitte auf der Grundlage des DQPM berechnet und bei der tatsächlichen Temperatur T und dem baryonischen chemischen Potential μB in jeder einzelnen Raum-Zeit-Zelle, in der die partonische Streuung stattfindet, ausgewertet werden.
Um die Spuren der μB-Abhängigkeit des QGPs in den Observablen zu untersuchen, werden die Ergebnisse von PHSD5.0 (mit μB-Abhängigkeiten) mit den Ergebnissen von PHSD5.0 für μB = 0 sowie mit PHSD4.0, in dem die Massen/Breiten der Quarks und Gluonen sowie deren Wechselwirkungsquerschnitte nur von T abhängen, verglichen. Wir diskutieren die PHSD-Ergebnisse für verschiedene Observablen: (i) Rapiditäts- und pT -Verteilungen von identifizierten Hadronen für symmetrische Au+Au- und Pb+Pb- Kollisionen bei Energien von 30 AGeV (zukünftige NICA-Energie) sowie für die RHIC-Spitzenenergie von √sNN = 200 GeV; (ii) gerichteter Fluss v1 von identifizierten Hadronen für Au + Au bei invarianter Energie √sNN = 27 GeV und 200 GeV; (iii) elliptischer Fluss v2 der identifizierten Hadronen für Au+Au bei invarianten Energien √sNN = 27 und 200 GeV. Der Vergleich der "Bulk"-Observablen für Au+Au-Kollisionen innerhalb der drei PHSD-Einstellungen hat gezeigt, dass sie eine recht geringe Empfindlichkeit gegenüber den μB -Abhängigkeiten der Partoneigenschaften (Massen und Breiten) und ihrer Wechselwirkungsquerschnitte aufweisen, sodass die Ergebnisse von PHSD5.0 mit und ohne μB sehr nahe beieinander liegen. Nur im Fall von Kaonen, Antiprotonen ̄p und Antihyperonen ̄Λ + ̄Σ0 konnte ein kleiner Unterschied zwischen PHSD4.0 und PHSD5.0 bei den höchsten SPS- und RHIC-Energien festgestellt werden.
Wir finden nur geringe Unterschiede zwischen den Ergebnissen von PHSD4.0 und PHSD5.0 für die hier betrachteten hadronischen Observablen sowohl bei hohen als auch bei mittleren Energien. Dies hängt damit zusammen, dass bei hohen Energien, wo die Materie vom QGP dominiert wird, ein sehr kleines chemisches Baryonenpotential μB in zentralen Kollisionen bei mittlerer Rapidität gemessen wird, während mit abnehmender Energie und größerem μB der Anteil des QGPs rapide abnimmt, sodass die endgültigen Beobachtungswerte insgesamt von den Hadronen dominiert werden, die an der hadronischen Rückstreuung teilgenommen haben, und somit die Information über ihren QGP-Ursprung verwaschen oder verloren geht.
In Kapitel 4 betrachten wir die Transportkoeffizienten von QGP-Materie im erweiterten Polyakov-NJL-Modell entlang der Übergangslinie für moderate Werte des chemischen Baryonenpotenzials 0 ≤ μB ≤ 0.9 GeV sowie in der Nähe des kritischen Endpunkts(CEP) und bei großem chemischen Baryonenpotenzial μB = 1.2 GeV, wo ein Phasenübergang erster Ordnung stattfindet. Wir untersuchen, wie die Natur der Freiheitsgrade die Transporteigenschaften des QGPs beeinflusst. Darüber hinaus demonstrieren wir die Auswirkungen des Phasenübergangs erster Ordnung und des CEP auf die Transportkoeffizienten im dekonfinierten QCD-Medium.
Darüber hinaus wird in Kapitel 5 eine phänomenologische Erweiterung des DQPM auf große baryonchemische Potentiale μB einschließlich der Region mit einem möglichen CEP und späterem Phasenübergang erster Ordnung betrachtet. Eines der wichtigsten Merkmale des Modells ist das Auftreten einer ’kritischen‘ Skalierung in der Nähe des CEP. Das Hauptziel des vorgestellten Modells besteht darin, die mikroskopischen und makroskopischen Eigenschaften der partonischen Freiheitsgrade für den Bereich des Phasendiagramms bereitzustellen, der durch moderates T und moderates oder hohes μB gekennzeichnet ist.
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Transport mechanism of a multidrug resistance protein investigated by pulsed EPR spectroscopy
(2019)
In human several diseases result from malfunctions of ATP-binding cassette (ABC) systems, which form one of the largest transport system superfamily. Many ABC exporters contain asymmetric nucleotide-binding sites (NBSs) and some of them are inhibited by the transported substrate.1 For the active transport of diverse chemically substrates across biological membranes, ABC transport complexes use the energy of ATP binding and subsequent hydrolysis. In this thesis, the heterodimeric ABC exporter TmrAB2,3 from Thermus thermophilus, a functional homolog of the human antigen translocation complex TAP, was investigated by using pulsed electron-electron double resonance (PELDOR/DEER) spectroscopy. In the presence of ATP, TmrAB exists in an equilibrium between inward- and outward-facing conformations. This equilibrium can be modulated by changing the ATP concentration, showing asymmetric behaviour in the open-to-close equilibrium between the consensus and the degenerate NBSs. At the degenerate NBS the closed conformation is more preferred and closure of one of the NBSs is sufficient to open the periplasmic gate at the transmembrane domain (TMD).3 By determining the temperature dependence of this conformational equilibrium, the thermodynamics of the energy coupling during ATP-induced conformational changes in TmrAB were investigated. The results demonstrate that ATP-binding alone drives the global conformational switching to the outward-facing state and allows the determination of the entropy and enthalpy changes for this step. With this knowledge, the Gibbs free energy of this ATP induced transition was calculated. Furthermore, an excess of substrate, meaning trans-inhibition of the transporter is resulting mechanistically in a reverse transition from the outward-facing state to an occluded conformation predominantly.3 This work unravels the central role of the reversible conformational equilibrium in the function and regulation of an ABC exporter. For the first time it is shown that the conformational thermodynamics of a large membrane protein complex can be investigated. The presented experiments give new possibilities to investigate other related medically important transporters with asymmetric NBSs or other similar protein complexes.
In this work we provided additional insights into our understanding of bulk QCD matter through the study of the transport coeffcients which govern the non-equilibrium microscopical processes of statistical ensembles. Specically, we focused on the low energy regime corresponding to the hadron gas, as the properties of this region of the phase diagram are still relatively unknown, and existing calculations for the transport coeffcients are either scarce, contradictory, or somewhat limited in scope; this thesis' main goal was thus to shed some light on this by providing new independent calculations of these quantities.
We subsequently presented two formalisms which can be used to calculate transport coeffcients. The first one (which also was the main tool we used in the following chapters to produce our results) relies on the development of so-called Green-Kubo formulas, which relate non-equilibrium dissipative fluctuations with transport coeffcients; notably, the off-diagonal components of the energy-momentum tensor are shown to be related to the shear viscosity, its diagonal components to the bulk viscosity and fluctuations in the electric current can be related to the electric conductivity. We additionally introduced two new conductivities, namely the baryon-electric and strange electric conductivities, which we dubbed, together with the already known electric one, the "cross-conductivity", which encodes information about how electric fluctuations are correlated to changes in electric, baryonic or strange currents, or vice-versa. The second way of calculating transport coeffcient which we discussed consists in linearizing the collision term of the Boltzmann equation through the Chapman-Enskog formalism. While in principle providing direct semi-analytical results for the transport coeffcients, this approach is complicated to implement when more than a few species are considered, and as such was then mostly used as a tool to calibrate our Green-Kubo calculations.
The hadron gas model that we used for all calculations, namely the transport approach SMASH, was then presented. The main features of the model were explained, such as the collision criterion, the considered degrees of freedom and the specific way in which they microscopically interact with each other. It was verified that SMASH does reproduce analytical results of the Boltzmann equation in an expanding universe scenario, thus showing the equivalence of this transport approach and the associated kinetic theory results. A special care was taken to detail the ways in which a state of thermal and chemical equilibrium (which is necessary for Green-Kubo relations to be valid) can be reached and described using SMASH.
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The TTL is the transition layer between the tropical troposphere and stratosphere, and is the main region where tropospheric air enters the stratosphere. In this thesis different transport processes are studied by using in situ measurements of tracers. Long-lived tracers were measured with the High Altitude Gas Analyzer (HAGAR) on board the M55 Geophysica aircraft. The instrument was developed by the University of Frankfurt and measures the long-lived tracers CO2, N2O, CFC-12, CFC-11, H-1211, SF6, CH4 and H2 with two gas chromatographic channels and a CO2 sensor (LICOR). The measurements are supported by CO and O3 measurements of other instruments. Two campaigns were conducted to obtain measurements in the TTL: SCOUT-O3 (November/December 2005 in Darwin, Australia) and AMMA-SCOUT-O3 (August 2006 in Ouagadougou, Burkina Faso). After a general introduction of the thesis in chapters one and two, the third chapter describes the findings during this last campaign. Five local flights are analyzed to study the different transport processes that occur in the tropical tropopause layer above West-Africa: deep convection up to the level of main convective outflow, vertical mixing after overshooting of air in deep convection, horizontal inmixing from the extratropical lower stratosphere, and horizontal transport across the subtropical barrier. Main findings are that the TTL over West-Africa is mostly influenced by remote convection. The subtropical barrier is not a strong barrier but more a region of transition between the extratropical and the tropical stratosphere. Chapter 4 presents the results obtained during the SCOUT-O3 campaign. From the eight local flights the last four flights (051129, 051130a, 051130b, 051205) show enhanced values of ozone, CO and CO2 between 355 and 380 K potential temperature in comparison with the first four flights (051116, 051119, 051123, 051125). Horizontal inmixing from the extra-tropical stratosphere and influence of the local convective system Hector cannot explain the enhanced values of the two flights on 30 November Therefore, other possible explanations for these enhanced CO, CO2 and ozone levels are proposed. The first explanation is vertical mixing in the vicinity of the jet stream. However, the jet cannot explain the differences between the flights on 30 November and the flights on 29 November and 5 December. Another possible explanation is influence of polluted boundary layer air masses from the Indonesian region. Especially air sampled during the flights on November 30 crossed large parts of northern Indonesia between 8 and 10 days before the measurements. Convective uplift of biomass burning and other pollution plumes can transport CO and ozone precursors into the upper troposphere, where they can significantly enhance the ozone production. The last chapter deals with the vertical ascent rate in the TTL and uses measurements of both the SCOUT-O3 and AMMA-SCOUT-O3 campaign as well as data from previous aircraft campaigns (TROCCINOX and APE-THESEO). Time scales and residence times for mean vertical transport in the background TTL are estimated for different seasons and over different geographic regions using in situ observations of CO2 and long-lived tracers. The vertical transport time scales are constrained using the seasonal variation of CO2 in the tropical troposphere as a “tracer clock” for vertical ascent. Two methods are applied to calculate the residence time in the layer between 360 and 390 K potential temperature. The first method uses the slope of the CO2 index, the second method fits the CO2 index directly to the measurements assuming a constant ascent rate. The first method yields residence times for Australia,West Africa, and Brazil of the same order, 35-45 days to 380 K and 50 days to 390 K (where no value can be derived for Australia as the slope is changing approximately one month before the campaign). For APE-THESEO, the method does not yield reasonable results. The best estimates using the second method show moderate residence times between 360 and 390 K of 60±25 days SCOUT-O3 (NH autumn) and 43±8 days for AMMA/SCOUT-O3 (NH summer). These results agree well with the results calculated using the first method. For APE-THESEO and TROCCINOX the best fits yield shorter residence times of 23±7 and 40±10 days, respectively, both during winter. These results correspond well to the expectations based on the seasonal variation of the Brewer-Dobson circulation.
The present work deals with the integration of variable renewable energy sources, wind and solar energy into the European and US power grid. In contrast to other networks, such as the gas supply mains, the electricity network is practically not able to store energy. Generation and consumption therefore always have tobe balanced. Currently, the load curve is viewed as a rigid boundary condition, which must be followed by the generation system. The basic idea of the approach followed here is that weather-dependent generation causes a shift of focus of the electricity supply. At high shares of wind and solar generation, the role of the rigid boundary condition falls to the residual load, that is, the remaining load after subtraction of renewable generation. The goal is to include the weather dependence as well as the load curve in the design of the future electricity supply.
After a brief introduction, the present work first turns to the underlying weather-, generation and load data, which form the starting point of the analysis. In addition, some basic concepts of energy economics are discussed, which are needed in the following.
In the main part of the thesis, several algorithms are developed to determine the load flow in a network with a high share of wind and solar energy and to determine the backup supply needed at the same time. Minimization of the energy needed from controllable power plants, the capacity variable power plants, and the capacity of storing serve as guiding principles. In addition, the optimization problem of grid extensions is considered. It is shown that it can be formulated as a convex optimization problem. It turns out that with an optimized, international transmission network which is about four times the currently available transmission capacity, much of the potential savings in backup energy (about 40%) in Europe can be reached. In contrast, a twelvefold increase the transmission capacity would be necessary for a complete implementation of all possible savings in dispatchable power plants.
The reduction of the dispatchable generation capacity and storage capacity, however, presents a greater challenge. Due to correlations in the generation of time series of individual countries, it may be reduced only with difficulty, and by only about 30%.
In the following, the influence of the relative share of wind and solar energy is illuminated and examined the interplay with the line capacitance. A stronger transmission network tends to lead to a higher proportion of wind energy being better integrated. With increasing line capacity, the optimal mix in Europe therefore shifts from about 70% to 80% wind. Similar analyses are carried out for the US with comparable results.
In addition, the cost of the overall system can be reduced. It is interesting at this point that the advantages for the network integration may outweigh higher production costs of individual technologies, so that it is more favourable from the viewpoint of the entire system to use the more expensive technologies.
Finally, attention is given to the flexibility of the dispatchable power plants. Starting from a Fourier-like decomposition of the load curve as it was a few years ago, when hardly renewable generation capacity was present, capacities of different flexibility classes of dispatchable power plant are calculated. For this purpose, it is assumed that the power plant park is able to follow the load curve without significant surplusses or deficits. From this examination, it is derived what capacity must at least be available without having to resort to a detailed database of existing power plants.
Assuming a strong European cooperation, with a stronger international transmission network, the dispatchable power capacity can be significantly reduced while maintaining security of supply and generating relatively small surplusses in dispatchable power plants.
Neurodevelopmental psychiatric disorders (NPDs) like attention deficit hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and schizophrenia, affect millions of people worldwide. Despite recent progress in NPD research, much remains to be discovered about their underpinnings, therapeutic targets, effects of biological sex and age. Risk factors influencing brain development and signalling include prenatal inflammation and genetic variation. This dissertation aimed to build upon these findings by combining behavioural, molecular, and neuromorphological investigations in mouse models of such risk factors, i.e. maternal immune activation (MIA), neuron-specific overexpression (OE) of the cytoplasmatic isoforms of the RNA-binding protein RBFOX1, and neuronal deletion of the small Ras GTPase DIRAS2.
Maternal infections during pregnancy pose an increased risk for NPDs in the offspring. While viral-like MIA has been previously established elsewhere, this study was the first in our institution to implement the model. I validated NPD-relevant deficits in anxiety- and depression-like behaviours, as well as dose- and sex-specific social deficits in mouse offspring following MIA in early gestation. Proteomic analyses in embryonic and adult hippocampal (HPC) synaptoneurosomes highlighted novel and known targets affected by MIA. Analysis of the embryonic dataset implicated neurodevelopmental disruptions of the lipid, polysaccharide, and glycoprotein metabolism, important for proper membrane function, signalling, and myelination, for NPD-pertinent sequelae. In adulthood, the observed changes encompassed transmembrane trafficking and intracellular signalling, apoptosis, and cytoskeletal organisation pathways. Importantly, 50 proteins altered by MIA in embryonic and adult HPC were enriched in the NPD-relevant synaptic vesicle cycle. A persistently upregulated protein cluster formed a functional network involved in presynaptic signalling and proteins downregulated in embryos but upregulated in adults by MIA were correlated with observed social deficits. 49/50 genes encoding these proteins were significantly associated with NPD- and comorbidity-relevant traits in human phenome-wise association study data for psychiatric phenotypes. These findings highlight NPD-relevant targets for future study and early intervention in at-risk individuals. MIA-evoked changes in the neuroarchitecture of the NPD-relevant HPC and prefrontal cortex (PFC) of male and female mice highlighted sex- and region-specific alterations in dendritic and spine morphology, possibly underlining behavioural phenotypes.
To further investigate genetic risk factors of NPDs, I performed a study based on the implications of RBFOX1’s pleiotropic role in neuropsychiatric disorders and previous preclinical findings. Cytoplasmatic OE of RBFOX1, which affects the stability and translation of thousands of targets, was used to disseminate its role in morphology and behaviour. RBFOX1 OE affected dendritic length and branching in the male PFC and led to spine alterations in both PFC and HPC. Due to previously observed ASD-like endophenotypes in our Rbfox1 KO mice and the importance of gene × environment effects on NPD susceptibility, I probed the interaction of cytoplasmatic OE and a low-dose MIA on offspring. Both RBFOX1 OE alone and with MIA led to increased offspring loss during the perinatal period. Preliminary data suggested that RBFOX1 OE × MIA might increase anxiety- and anhedonia-like behaviours. Morphological changes in the adult male OE HPC and PFC suggested increased spine density and reduced dendritic complexity. A small post-mortem study in human dorsolateral PFC of older adults did not reveal significant effects of a common risk variant on RBFOX1 abundance.
To expand upon NPD genetic risks, I evaluated the effects of a homo- (KO) or heterozygous (HET) Diras2 deletion in a novel, neuron-specific mouse model. DIRAS2’s function is largely unknown, but it has been associated with ADHD in humans and neurodevelopment in vitro. In adult mice, there were subtle sex-specific effects on behaviour, i.e. more pronounced NPD-relevant deficits in males, in keeping with human data. KO mice had subtly improved cognitive performance, while HET mice exhibited behaviours in line with core ADHD symptoms, e.g. earning difficulties (females), response inhibition deficits and hyperactivity (males), suggesting Diras2 dose-sensitivity and sex-specificity. The morphological findings revealed multiple aberrations in dendritic and spine morphology in the adult PFC, HPC, and amygdala of HET males. KOs changes in spine and dendritic morphology were exclusively in the PFC and largely opposite to those in HETs and NPD-like phenotypes. Region- and genotype-specific expression changes in Diras2 and Diras1 were observed in six relevant brain regions of adult HET and KO females, also revealing differences in the survival and morphology regulator mTOR, which might underlie observed differences.
In conclusion, the effects of MIA and partial Diras2 knockdown resembled each other in core, NPD-associated behavioural and morphological phenotypes, while cytoplasmatic RBFOX1 OE and full Diras2 KO differed from those. My findings suggest complex dose- and sex-dependent relationships between these prenatal and genetic interventions, whose NPD-relevant influences might converge onto neurodevelopmental molecular pathways. An assessment of such putative overlap, based on available data from the MIA proteomic analyses of embryonic and adult HPC, suggested the three models might be linked via downstream targets, interactions, and upstream regulators. Future studies should disseminate both distinct and shared aspects of MIA, RBFOX1, and DIRAS2 relevant to NPDs and build upon these findings.
Inflammation is a regulated reaction of the body to control a threat such as infection or injury. An efficient resolution of inflammation is critical to prevent the development of chronic inflammation and to restore tissue homeostasis. Macrophages (Mf) play a crucial role in the onset, but also in the resolution of inflammation, because they phagocytose and eliminate pathogens and tissue debris. Efficient efferocytosis, i.e. the engulfment of apoptotic cells, represents an important trigger for the onset of the resolution response and contributes to the pro-resolving reprogramming of Mf. Despite the importance of post- transcriptional modes of regulation during the resolution phase and translational control as a key node modulating gene expression in immune cells, relevant translational alterations remain largely elusive.
In the present study, I aimed to identify translationally regulated targets in inflammatory primary murine Mf upon resolution-promoting efferocytosis. To this end, I used total RNA-sequencing as well as de novo proteomics analyses to determine global transcriptional and translational changes. Sequencing data confirmed that efferocytosis induced a pro-resolution signature in inflammatory Mf and pointed towards translational regulation because the related integrated stress response was enriched upon efferocytosis. While changes of gene expression between efferocytic and non-efferocytic Mf appeared rather small at the transcriptional level, I observed considerable differences at the level of de novo synthesized proteins. This finding suggests a regulation at the level of translation. Furthermore, the tight connection between translational and metabolic changes was confirmed by enriched metabolism-associated terms of targets upregulated by efferocytosis at both RNA and de novo protein level. Interestingly, analysis of translationally regulated targets in response to inflammatory stimulation showed reduced translation for most targets, with only little impact of efferocytosis. Among those targets, I identified pro-resolving matrix metallopeptidase 12 (Mmp12) as a novel candidate, which showed translational repression during early inflammation and translational increase during the resolution phase. Noteworthy, a first indicator for a potential translation regulatory component of Mmp12 were the extremely high mRNA levels and not overly high de novo protein levels. Validation experiments recapitulated a slight elevation of Mmp12 mRNA expression and a significant downregulation of MMP12 intracellular protein levels in inflammatory Mf, as observed in the RNA-seq and de novo proteomics datasets. To investigate whether the discrepancy in mRNA and protein expression were due to changes in translation, I applied polysomal fractionation analysis to determine the translational status of Mmp12. Inflammatory Mf displayed a significantly lower relative Mmp12 mRNA abundance in the late polysomes compared to naïve Mf, suggesting reduced translational efficiency upon inflammatory stimulation. Consequently, extracellular MMP12 levels in the supernatant of inflammatory Mf decreased, although with a slight delay.
The functional impact of attenuated Mmp12 translation upon inflammatory stimulation was assessed in migration assays. While siRNA-mediated knockdown of Mmp12 did not alter Mf migration on uncoated plates, it increased migration 3-fold on matrigel/elastin-coated plates. Importantly, the increase in migrated distance driven by siMmp12 could be lowered by the addition of exogenous recombinant MMP12 protein. In line with reduced Mmp12 translation and MMP12 protein in inflammatory Mf, I observed a significant increase in cell migration on matrigel/elastin-coated plates, while it remained unaltered on uncoated plates. Consequently, Mf elastase MMP12 degrades elastin, thereby cell migration along elastin fibers is diminished. In inflammatory Mf, Mmp12 is translationally downregulated, thereby enhancing the migratory capacity.
In summary, the present study identifies a substantial contribution of translational regulation in the course of inflammation shown by high changes between inflammatory naïve and efferocytic Mf at the de novo proteomic level. Specifically, I was able to determine the translational regulation of pro-resolving Mmp12, which is repressed during early inflammation and recovers during the resolution phase. Functionally, translational control of MMP12 emerged as a strategy to alter the migratory properties of Mf, enabling enhanced, matrix- dependent migration of Mf during the early inflammatory phase, while restricting migration during the resolution phase.
Languages in general have various possibilities to express one and the same propositional content. One of these possibilities is grammatical variation. This thesis is concerned with the variation of the linear word order in a clause and the effects triggered by word order alternations. Although sharing the same propositional content, different word order variants can carry different functions; word order variation can be used to achieve certain stylistic effects. The dissertation looks at functional and stylistic preferences of English regarding variation from the canonical word order in (1).
(1) [Ernie]S [sits]V [on the table]O. (SVO)
The variation under consideration is locative inversion (LOCI), exemplified in (2).
(2) On the table sits Ernie.
As any variation from the canonical word order is said to strongly depend on the grammatical system of the language a sentence is realized in, the perspective is extended to the word order equivalent of the sentence above in German (3). The goal is to highlight possible differences/similarities between English and German with respect to one specific word order variant in a declarative main clause.
(3) Auf dem Tisch liegt ein Brief.
On the table lies a letter
‘On the table lies a letter’.
As the variation from the canonical word order is not expected to be coincidental in both languages, the features that favor the pattern under consideration are examined. This is done through a statistical analysis by employing two comparable corpora, the BNC for English and the TÜPP D/Z for German. The central questions for the thesis therefore are: What are the functions of the inverted constructions in English and German, what features favor their use in the respective languages, and how are they realized syntactically?
One finding is that German uses the syntactic pattern PP-V-NP for very similar reasons this pattern is used for in English. There seems to be a general tendency to order shorter before longer constituents. The syntactic pattern under consideration fulfills similar discourse functions in both languages. Both languages show similar preferences, they are driven by similar factors when having to decide on whether to stay with the canonical order or to prepose (respectively invert) the canonically postverbal PP.
This study analyses five British translations of Bertolt Brecht's 'Mutter Courage und ihre Kinder'. Two of these translations were written by speakers of German, and three by well-known British playwrights with no knowledge of the source text language. Four have been produced in mainstream British theatres in the past twenty-five years. The study applies translation studies methodology to a textual analysis which focuses on the translation of techniques of linguistic "Verfremdung", as well as linguistic expression of the comedy and of the political dimension in the work. It thus closes the gap in current Brecht research in examining the importance of his idiosyncratic use of language to the translation and reception of his work in the UK. The study assesses the ways in which the translator and director are influenced by Brecht's legacy in the UK and in turn, what image of Brecht they mediate through the production on stage. To this end, the study throws light on the formation of Brecht's problematic reputation in the UK, and it also highlights the social and political circumstances in early twentieth century Germany which prompted Brecht to develop his theory of an epic theatre. The focus on a linguistic examination allows the translator's contribution to the production process to be isolated. Together with an investigation of the reception of each performance text, this in turn facilitates a more accurate assessment of the translator and director's respective influence in the process of transforming a foreign-language text onto a local stage. The analysis also sheds light on the different approaches taken by speakers of German, and playwrights creating an English version from a literal translation. It pinpoints losses in translation and adaptation, and suggests how future versions may avoid these.
The marginalization of the hijra identity in postcolonial Pakistan perpetuates the inequalities that have dogged the transgender community since the colonial era. Although Pakistan has since ratified all concerned UN treaties aimed at protecting transgender people and preventing human rights violations against them, the country’s gender-variant population nevertheless remains vulnerable to these transgressions. As such, this study aims to explore the following inquiry: “What are the lifeways of the hijra community and how do hijra people face human rights violations in their daily life activities?”
The identity construction of the hijra is a complex process. Pakistan is a patriarchal society that determines gender based on biological sex. While a genitally ambiguous child is generally recognized as intersexed, the family usually obscures this circumstance or tries to enforce a predominantly male identity onto the child. To some degree, an intersexed child is allowed to perform feminine roles, particularly when compared to a biologically male individual who is inclined toward femininity. They may partake in “girls’ games” or in “women’s chores” like cooking; they may opt to don feminine clothing and jewelry or practice walking and talking “like a girl.” Many family members and relatives consider such actions a threat to family honor and/or an indication of weakness, which in turn renders the child vulnerable to sexual or physical assault. Abuse also causes some gender-variant children to drop out of school. As adults, many hijras do not see childhood sexual encounters as assault, particularly because they considered themselves to be feminine even from a young age. Nevertheless, experiences of isolation, abuse, and exclusion often compel a gender-variant child to seek company outside of his/her family of orientation.
Many transgender individuals see redemption in joining the hijra community: there, a new identity is defined and shaped. New members mirror themselves after more senior hijras. In the community, relationships are solidified through similar childhood experiences and interests as well as a shared freedom to express the outer reflection of an “inner feminine soul.” Here, they accept the childhood label affixed to them by heteronormative society: hijra. In fact, the identity now becomes the key to economic viability and socialization.
The predominant livelihood strategies within the hijra community are dancing and prostitution. New members must adhere to stringent norms and rules; they risk (sometimes severe) punishment if they do not. For example, a new hijra must adopt a very strict feminine appearance; if she does not appear feminine enough she may be socially isolated or physically punished. Similarly, a hijra is required to remain passive during sex. In fact, because hijras are stereotyped as passive and vulnerable, many clients physically exploit or even rape them. If she tries to resist, a hijra may face physical violence and, in extreme circumstances, death. Reporting abuse to law enforcement authorities often leads to further exploitation. As such, whether dancing or performing sexually, hijras are encouraged to do whatever is asked of them.
In the last decade, the Supreme Court of Pakistan has taken significant steps to ensure the rights of transgender people. The Court has similarly compelled local governments to amend existing legislation in order to protect the transgender community. Nevertheless, discrepancies exist in legislative and judicial interpretations of the transgender identity, which continues to impede the struggle for basic rights. Indeed, there is a long way to go in the effort to incorporate transgender people into the folds of mainstream Pakistani society.
To date it is not clear at which stage of differentiation mature T cell leukaemia/lymphoma is initiated. Previous studies in our group showed that mature T cells are relatively resistant to transformation. We wanted to further investigate the transformation potential of NPM-ALK, p21SNFT and the viral oncoprotein Tax on mature T cells. First, we analyzed the effects on T cell growth in vitro after transducing human T cell lines with gammaretroviral vectors encoding these genes. No growth or proliferation promoting effect of all three genes was observed. In the second part of the project, we transduced murine, mature T cells and/or haematopoietic stem cells (HPCs/HSCs) and transplanted these cells into Rag-1 deficient recipients. All mice transplanted with NPM-ALK transduced monoclonal mature T cells (OT-1) developed leukaemia/lymphoma. In contrast, only few NPM-ALK transduced polyclonal T cell and HPC/HSC transplanted mice developed leukaemia/lymphoma. From the p21SNFT group, only two mice transplanted with transduced OT-1 T cells developed leukaemia/lymphoma, which showed high eGFP and interestingly CD19 expression. No malignancies were observed in Tax transplanted animals so far. Furthermore, the recipients do not show any eGFP marking in the periphery. In conclusion, our results show that compared to polyclonal T cells, monoclonal T cells are transformable after gammaretroviral transfer of NPM-ALK and p21SNFT.
Across the entire animal kingdom, sociality, i.e. the tendency of individual animals to form a group with conspecifics, is a common trait. Environmental changes have to be met with corresponding, quick adaptations. For social species, the presence of conspecifics is important for survival and if social animals are deprived of access to conspecifics, this can lead to strong and lasting changes on a physiological level as well as behaviour. Gene expression changes responsible for these adaptations have so far not been understood in detail. As social isolation leads to changes on a neuronal level, it is important to investigate the gene expression changes that are induced in the brain. In this thesis, next-generation RNA-sequencing was applied to zebrafish, a well-established model organism characterized by its high degree of companionship. Within the entire brain, gene expression was analysed in zebrafish that were raised either with conspecifis or in isolation, ranging from 5 to 21 days post fertilization. Using this approach, several genes were identified that were downregulated by social isolation. In this thesis, I focused on one of these consistently downregulated genes, parathyroid hormone 2 (pth2). The expression of pth2 was demonstrated to be bidirectionally regulated by the number of conspecifics present and to be responsive to changes in the social environment within 30 minutes. Regulation of pth2 does not occur by visual or chemosensory access to conspecifcs, but is mediated by mechanosensory perception of other fish via the lateral line. In an experiment using an artificial mechanical stimulation paradigm, it was shown that the features necessary to elicit pth2 transcription closely mimick the locomotion of actual zebrafish. Other, similar stimulation paradigms are not capable to induce this transcriptional response.
Die Bildung von Blutgefäßen ist essentiell für die Entwicklung und Homöostase von Wirbeltieren und die Endothelzellspezifikation ist ein wichtiger erster Schritt in diesem Prozess. Das früheste bekannte Ereignis bei der Endothelzellspezifikation im Zebrafisch ist die Expression des bHLH-PAS-Transkriptionsfaktor-Gens npas4l. Ich habe eine transgene V5-Linie zum Nachweis des markierten Npas4l auf Proteinebene und eine Gal4-VP16-Reporterlinie zur Visualisierung und Verfolgung von npas4l exprimierenden Zellen in vivo generiert. Beide Linien können bereits in frühen Entwicklungsstadien nachgewiesen werden und komplementieren auch starke npas4l-Mutanten Allele. Um npas4l Reporter exprimierende Zellen in npas4l Mutanten zu verfolgen, habe ich anschließend eine mutierte Variante der Gal4-Reporterlinie erzeugt. Diese Mutante trägt eine Insertion in der Region, die die DNA-Bindedomäne kodiert. Dadurch stört sie die Npas4l-Funktion, aber nicht die Reporterexpression. Dieses mutierte Reporterallel komplementiert nicht die npas4l-Mutanten und zeigt einen starken Phänotyp, was darauf hindeutet, dass es sich um ein funktionelles Nullallel handelt. Phänotypische Analysen zeigten, dass npas4l-Reporter positive Zellen in npas4l-Mutanten nicht spezifizieren oder zur Mittelachse wandern. Stattdessen tragen sie zu den vom intermediären Mesoderm abgeleiteten pronephrischen Tubuli und dem vom paraxialen Mesoderm abgeleiteten Skelettmuskel bei. Ich habe diese Phänotypen durch Einzelzell-RNAseq an den npas4l-Reporter positiven Zellen in npas4l+/- und npas4l-/- Embryonen bestätigt. Zusammen erklären diese beiden alternativen Zellschicksale den Großteil der beobachteten Veränderungen zwischen den Genotypen. Npas4l ist dafür bekannt die Expression der drei Transkriptionsfaktorgene etsrp, tal1 und lmo2 zu fördern. Ich stellte die Hypothese auf, dass das Fehlen jedes dieser Transkriptionsfaktoren in npas4l-Mutanten verschiedene Aspekte des npas4l-Phänotyps verursacht. Daher habe ich Mutantenlinien für alle drei Gene generiert und sie sowohl in vaskulären Reporterlinien als auch im npas4l-Reporterhintergrund analysiert. Die Daten legen nahe, dass verschiedene Gene unterschiedliche Prozesse während der frühen Endothelentwicklung regulieren. In npas4l-/- und etsrp-/- Embryonen differenzieren npas4l-Reporter exprimierende Zellen nicht zu Endothelzellen und tragen stattdessen zur Skelettmuskelzellpopulation bei. In npas4l-/- und tal1-/- Embryonen können npas4l-Reporter exprimierende Zellen nicht migrieren und tragen stattdessen zu der Bildung der pronephrischen Tubuli bei. Um die Beziehung zwischen diesen Faktoren besser zu verstehen, habe ich getestet, ob die Injektion von etsrp-, tal1- oder lmo2-mRNA verschiedene Aspekte des npas4l-Phänotyps retten würde. npas4l-, etsrp- und tal1-Mutanten zeigen alle schwere vaskuläre Phänotypen. Einige Endothelzellen und vaskuläre Strukturen bleiben jedoch in jeder Mutante erhalten. Der Phänotyp ist am stärksten in npas4l-/- Embryonen, aber selbst in diesen Embryonen können einige fli1a-positive Endothelzellen in der Schwanzregion beobachtet werden. Es war unklar, ob sich diese Population von Endothelzellen unabhängig von der Npas4l-, Tal1- und Etsrp-Funktion entwickelt oder als Folge einer restlichen tal1- oder etsrp-Expression unabhängig von Npas4l. Um diese Frage zu untersuchen, habe ich Doppelmutanten generiert und nach dem Vorhandensein von fli1a-positiven Endothelzellen in diesen Mutanten gesucht. Während fli1a-positive Endothelzellen in npas4l-/- und npas4l-/-;tal1-/- Embryonen deutlich vorhanden sind, können keine solchen Zellen in npas4l-/-;etsrp-/- oder etsrp-/-;tal1-/- Embryonen beobachtet werden. Diese Daten deuten darauf hin, dass sich im Zebrafisch keine Endothelzellen entwickeln können, wenn zugleich npas4l und etsrp oder etsrp und tal1 gestört sind. Während der Verlust von etsrp zu stärkeren Defekten in npas4l-Mutanten führt, gibt es keinen zusätzlichen Phänotyp, der durch den Verlust von tal1verursacht wird, was darauf hindeutet, dass die Expression von etsrp, aber nicht die von tal1, unabhängig von Npas4l auftreten kann. Diese Idee wird durch die Beobachtung unterstützt, dass etsrp, aber nicht tal1-Expression in den meisten fli1a-exprimierenden Zellen in npas4l-/- Embryonen beobachtet wird. Dennoch wird der Großteil -Expression durch Npas4l reguliert. tal1-mRNA-Injektionen reichten aus, um eine Wildtyp-ähnliche vaskuläre Musterbildung im Bauchbereich der npas4l-/- Embryonen wiederherzustellen, einschließlich der Rettung sowohl der Zellmigration als auch der Differenzierung. Da Npas4l mehrere unterschiedliche transkriptionelle Effektoren hat, war eine so starke Rettung durch nur einen dieser Effektoren unerwartet. In den geretteten Mutanten wurde die bilaterale Population von npas4l-Reporter-positiven pronephrischen Tubuluszellen nicht entdeckt, aber die Anzahl der ektopischen npas4l-Reporter exprimierenden Muskelzellen war im Vergleich zu nicht injizierten npas4l-Mutanten gleichbleibend.
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Trait-dependent effects of biotic and abiotic filters on plant regeneration in Southern Ecuador
(2024)
Tropical forests have always fascinated scientists due to their unique biodiversity. However, our understanding of ecological processes shaping the complexity of tropical rainforests is still relatively poor. Plant regeneration is one of the processes that remain understudied in the tropics although this is a key process defining the structure, diversity and assembly of tropical plant communities. In my dissertation, I combine experimental, observational and trait-based approaches to identify processes shaping the assembly of seedling communities and compare associations between environmental conditions and plant traits across plant life stages. By working along a steep environmental gradient in the tropical mountains of Southern Ecuador, I was able to investigate how processes of plant regeneration vary in response to biotic and abiotic factors in tropical montane forests.
My dissertation comprises three complementary chapters, each addressing an individual research question. First, I studied how trait composition in plant communities varies in relation to the broad- and local-scale environmental conditions and across the plant life cycle. I measured key traits reflecting different ecological strategies of plants that correspond to three stages of the plant life cycle (i.e., adult trees, seed rain and recruiting seedlings). I worked on 81 subplots along an elevational gradient covering a large climatic gradient at three different elevations (1000, 2000 and 3000 m a.s.l.). In addition, I measured soil and light conditions at the local spatial scale within each subplot. My findings show that the trait composition of leaves, seeds and seedlings changed similarly across the elevational gradient, but that the different life stages responded differently to the local gradients in soil nutrients and light availability. Consequently, my findings highlight that trait-environment associations in plant communities differ between large and small spatial scales and across plant life stages.
Second, I investigated how seed size affects seedling recruitment in natural forests and in pastures in relation to abiotic and biotic factors. I set up a seed sowing experiment in both habitat types and sowed over 8,000 seeds belonging to seven tree species differing in seed size. I found that large-seeded species had higher proportions of recruitment in the forests compared to small-seeded species. However, small-seeded species tended to recruit better in pastures compared to large-seeded species. I showed that high surface temperature was the main driver of differences in seedling recruitment between habitats, because it limited seedling recruitment of large-seeded species. The results from this experiment show that pasture restoration requires seed addition of large-seeded species and active protection of recruiting seedlings in order to mitigate harmful conditions associated with high temperatures in deforested areas.
Third, I examined the associations between seedling beta-diversity and different abiotic and biotic factors between and within elevations. I applied beta-diversity partitioning to obtain two components of beta-diversity: species turnover and species richness differences. I associated these components of beta-diversity with biotic pressures by herbivores and fungal pathogens and environmental heterogeneity in light and soil conditions. I found that species turnover in seedling communities was positively associated with the dissimilarity in biotic pressures within elevations and with environmental heterogeneity between elevations. Further, I found that species richness differences increased primarily with increasing environmental heterogeneity within elevations. My findings show that the associations between beta-diversity of seedling communities and abiotic and biotic factors are scale-dependent, most likely due to differences in species sorting in response to biotic pressures and species coexistence in response to environmental heterogeneity.
My dissertation reveals that studying processes of community assembly at different plant life stages and spatial scales can yield new insights into patterns and processes of plant regeneration in tropical forests. I investigated how community assembly processes are governed by abiotic and biotic filtering across and within elevations. I also experimentally explored how the process of seedling recruitment depends on seed size-dependent interactions, and verified how these effects are associated with abiotic and biotic filtering. Identifying such processes is crucial to inform predictive models of environmental change on plant regeneration and successful forest restoration. Further exploration of plant functional traits and their associations with local-scale environmental conditions could effectively support local conservation efforts needed to enhance forest cover in the future and halt the accelerating loss of biodiversity.
The current work investigated the association of trait anxiety and the neural efficiency of cognitive processing for affectively neutral (not threat-related) information. In a sample of 46 healthy volunteers, three fMRI experiments were conducted to test the prediction derived from attentional control theory (Eysenck et al., 2007) that high as compared to low trait-anxious individuals expend more neural effort on tasks requiring the top-down control of attention to reach a given level of performance. In a colour-word Stroop task requiring the inhibition of irrelevant stimulus information and associated responses as well as in a working-memorymanipulation task requiring the shifting of attention between items in working memory, trait anxiety (as measured with the State-Trait Anxiety Inventory; Spielberger et al., 1970) was positively associated with task-related increases in the activation of two adjacent regions in the right dorsolateral prefrontal cortex (DLPFC). The finding that along with a stronger activation of this brain region commonly implicated in top-down control processes, the high-anxious subjects showed equal (working memory manipulation) or worse (Stroop) performance when compared to low-anxious subjects, does support the assumption that processing is less efficient in the high anxious. However, in contrast to the predictions, trait anxiety did not show a significant association with task-related brain activation in a task-switching paradigm requiring shifting between task sets. It is discussed how different attentional control demands of the task may account for differences in the effects of trait anxiety on overt behavioural performance and underlying neural processes. In addition to DLPFC activation, trait anxiety modulated the functional connectivity of distributed regions involved in processing of the Stroop and the working-memory-manipulation task. It is discussed how the observed differences in regional DLPFC activation and network connectivity relate to each other. A possible interpretation suggests that activation increases in the DLPFC reflect an attempt to compensate for suboptimal connectivity by investing more effort in prefrontally supported control processes. Overall, the current work shows an association of trait anxiety with the neural efficiency of cognitive processing in affectively neutral tasks involving attentional control. Furthermore, it suggests that investigations of neural efficiency should take into account difference in functional integration in addition to regional activation.
A sound and well-functioning legal system will encourage growth in investment and create opportunities for investors. Trademarks as part of intellectual property play an important role in the future development of a country. A mark or symbol is needed in order to give products and services identity and to distinguish them and their qualities from identical or similar products and services of a competitor.
This research studies, examines and analyses the degree, nature and function of trademark protection within the legal system of Afghanistan and compare them with the Paris, Madrid and TRIPs agreements. It has been divided into four chapters: Chapter one provides general information and an overview of the current legal system of Afghanistan. Chapter two studies and analyses international agreements pertaining to the legal protection of trademark. It also critically assesses the ATML compatibility with these agreements: and answers the research question of to what extent the ATML provisions are compatible with them. Chapter three provides information on the different purposes of trademarks from a development perspective and compares the purposes provided by the ATML. Finally, chapter four assesses and examines the acquisition, assignment and termination of trademarks. The conclusions and findings of the thesis are the final section of this research.
Afghanistan, as a transitioning economy, has not developed a solid legal and practical foundation for providing comprehensive protection mechanisms for trademarks as have been articulated in developed countries and international agreements. Accordingly, the Afghan government has not entirely integrated these needs into its legal system and there are some inconsistencies of the ATML with these agreements.
One more challenge is the lack of appropriate legal institutions for issuing, managing, administering and protecting of trademarks. The establishment of a well-functioning administrative institution will serve to fulfil the objectives of the laws. Therefore, the CBR office holds the administrative responsibility for processing the registration of trademarks.
However, the methods and facilities of the CBR office remain outdated, and the office does not have the capacity to provide applicants with up-to-date administrative and technical facilities.
Therefore, legal protection of trademark in Afghanistan is linked not only to the existence of a well functioning of laws, regulations, clear procedures, mechanism and guidelines but also to an efficient and well-functioning administrative office.
Die Dissertation kombiniert die Methode der funktionellen Magnetresonanztomographie (fMRT) zur genauen räumlichen Lokalisation aufgabenkorrelierter parietaler Aktivierungen mit Transkranieller Magnetstimulation (TMS) zur systematischen Untersuchung der funktionellen Relevanz dieser Aktivierungen für die tatsächliche Leistungsfähigkeit. Die experimentelle Kombination beider Methoden ermöglichte die gezielte Stimulation der im tMRT identifizierten, mit visuospatialen Fähigkeiten assoziierten Hirnareale. Durch die systematische Auswertung der TMS-induzierten visuospatialen Leistungsveränderungen wurde die spezifische funktionelle Bedeutung dieser Hirnareale für visuospatiale Leistungen experimentell untersucht. Der zugrunde gelegte Versuchsplan umfasste sowohl visuospatiale Leistungen auf der Grundlage visuell dargebotener als auch mental vorgestellter Aufgaben. Dies ermöglichte die systematische Untersuchung, ob und inwieweit mentale visuospatiale Informationsverarbeitung die gleichen oder ähnliche Aktivierungsmuster im fMRT aufweist wie visuospatiale Verarbeitung visuell dargebotener Stimuli, und ob sich diese Aktivierungsmuster vorgestellter Stimuli unter dem Einfluss von rTMS in gleicher Weise als funktionell relevant erweisen. Aufgrund der separaten unilateralen Stimulation beider Hemisphären konnten darüber hinaus die unterschiedlichen behavioralen Auswirkungen einer Aktivierungsunterdrückung des linken und rechten Parietalkortex systematisch untersucht werden. Obwohl die Ausführung visuospatialer Aufgaben, sowohl auf der Grundlage visuell dargebotener als auch mental vorgestellter Stimuli, im fMRT mit einer bilateralen Aktivierung im Parietalkortex korrelierte, führte lediglich die TMS-induzierte temporäre Unterbrechung der neuronalen Aktivierung im rechten Parietalkortex zu einer signifikanten Verschlechterung in der Leistungsfähigkeit der damit assoziierten visuospatialen Aufgaben. Auf der Grundlage dieser Ergebnisse wurde ein modulares Modell der visuospatialen Imagination formuliert, in welchem den aufgabenkorrelierten bilateralen Aktivierungen aufgrund ihrer raum-zeitlichen Separierbarkeit unterschiedliche mentale Prozesse und aufgrund der mit TMS aufgezeigten funktionellen hemisphärischen Asymmetrie parietaler Aktivierung für visuospatiale Informationsverarbeitung unterschiedliche Kompensationsmechanismen zugeordnet wurden.
The metabolome of any live cell consists of several hundred, if not thousands of different molecules at any given moment, be it a relatively small bacterial cell or a whole multicellular organism. Although there are continuous attempts to differentiate between primary and secondary metabolites, the borders often blur in the eye of almost perfect interconvertability of all such matter. With chemistry and physics dominating this domain of biology it is an interdisciplinary endeavor to tackle the questions surrounding the workings of the metabolic pathways involved, searching for answers that ultimately help us to better understand life and find solutions to problems that affect us humans. One area of biochemistry that serves as a formidable example of the intertwined primary and secondary metabolic pathways are fatty acids, essential components of bacterial membranes, sources of energy and carbon but also important building blocks of several natural products. The second area to be mentioned is the metabolism of amino acids, the basic components of proteins and enzymes, which also serve as precursors to a diverse set of metabolites with many biological purposes.
This work focuses on these two areas of biochemistry, as several intermediates of their metabolism serve as building blocks for complex secondary metabolites whence many interesting and bioactive natural products are derived. The powerful and relatively novel tool of click-chemistry is employed to track azide-labeled precursors of primary and secondary metabolism in various bacterial strains to observe biochemistry at work and adds to the knowledge gained through other methods. The methods presented in this work serve the observation of fatty acid biosynthesis, degradation, modification and transport through direct ligation of azido fatty acids with cyclooctynes on one hand, leading to a revision of fatty acid transport in general. On the other hand a cleavable azide-reactive resin is devised to generally track the fate of azidated compounds through the myriads of metabolic pathways offered by entomopathogenic bacteria possessing a rich secondary metabolism. The resulting findings led to the identification of several antimicrobial peptides, amides and other compounds of which many had remained so far undetected in the strains that underwent investigation, underlining the worth of this method for future metabolomic research and beyond.
The metabolome of any live cell consists of several hundred, if not thousands of different molecules at any given moment, be it a relatively small bacterial cell or a whole multicellular organism. Although there are continuous attempts to differentiate between primary and secondary metabolites, the borders often blur in the eye of almost perfect interconvertability of all such matter. With chemistry and physics dominating this domain of biology it is an interdisciplinary endeavor to tackle the questions surrounding the workings of the metabolic pathways involved, searching for answers that ultimately help us to better understand life and find solutions to problems that affect us humans. One area of biochemistry that serves as a formidable example of the intertwined primary and secondary metabolic pathways are fatty acids, essential components of bacterial membranes, sources of energy and carbon but also important building blocks of several natural products. The second area to be mentioned is the metabolism of amino acids, the basic components of proteins and enzymes, which also serve as precursors to a diverse set of metabolites with many biological purposes.
This work focuses on these two areas of biochemistry, as several intermediates of their metabolism serve as building blocks for complex secondary metabolites whence many interesting and bioactive natural products are derived. The powerful and relatively novel tool of click-chemistry is employed to track azide-labeled precursors of primary and secondary metabolism in various bacterial strains to observe biochemistry at work and adds to the knowledge gained through other methods. The methods presented in this work serve the observation of fatty acid biosynthesis, degradation, modification and transport through direct ligation of azido fatty acids with cyclooctynes on one hand, leading to a revision of fatty acid transport in general. On the other hand a cleavable azide-reactive resin is devised to generally track the fate of azidated compounds through the myriads of metabolic pathways offered by entomopathogenic bacteria possessing a rich secondary metabolism. The resulting findings led to the identification of several antimicrobial peptides, amides and other compounds of which many had remained so far undetected in the strains that underwent investigation, underlining the worth of this method for future metabolomic research and beyond.
The mammalian family of bears (Ursidae) comprises eight extant species, occurring on four different continents. Among them are the iconic and well-known brown and polar bears, both widely distributed across the Northern hemisphere. Their intraspecific genetic structuring has been extensively investigated, albeit with a focus on genetic markers from maternally inherited parts of their genomes (mitochondrial DNA). The evolutionary relationship and divergence time between brown and polar bears have recently triggered an extensive debate, while less focus has been put on to other parts of the ursid phylogeny, particularly to a clade of three Asian bear species. To date, whole genomes of more than 100 bear individuals from four different species have been sequenced. Yet, one fundamental part of the genome has been largely omitted from specific analyses, in bears as well as in most other mammals: the Y chromosome.
The mammalian Y chromosome provides a unique perspective on the evolutionary history of organisms due to its distinct features, and specifically reflects the patriline because of its male-specific inheritance. The characteristics of this chromosome make it well suited to complement and contrast evolutionary inferences based on other genetic markers, and to uncover processes like sex-biased gene flow and hybridization. The unique insights that can be gained from analyses of Y-linked genetic variation made me utilize this part of the genome to investigate the evolution of male lineages in bears. Studying the patriline is particularly promising in this taxonomic group because of male-biased dispersal and a complex and fast radiation of bears. The analysis of Y-chromosomal genetic markers is thus the common theme of this dissertation: I present the identification of large amounts of Y-chromosomal sequence, the development of male-specific markers from such sequences, and the application of these markers to trace the evolution of male lineages of different bear species.
Specifically, I developed a molecular sex determination system based on the detection of two Y-linked fragments that allows to reliably discriminate between females and males from seven different bear species (Bidon et al. 2013). The approach is highly sensitive, bear-specific, and can be applied in standard molecular laboratories. This makes it valuable in conservation genetics and forensic applications, e.g. to analyze non-invasively collected samples.
Furthermore, I used Y-linked markers in a comprehensive and range-wide sample of brown and polar bears, and show that male-biased gene flow plays an important role in distributing genetic material throughout the ranges of both species (Bidon et al. 2014). In brown bears, I detected a lack of paternal population structuring which is in strong contrast to the detailed structuring of the matriline.
Analyzing Y-chromosomal sequences from all eight bear species, I present a phylogeny of the patriline that largely resembles the topology from other nuclear markers but is different from the topology of the mitochondrial gene tree (Kutschera et al. 2014). This discordance among loci generates interesting hypotheses about inter-species gene flow, particularly among American and Asiatic black bears.
With the identification of almost two million basepairs of Y-chromosomal sequence and the analysis of an unprecedented large male-specific dataset in polar bears, a high-resolution view on the distribution of their intraspecific variation was obtained (Bidon et al. 2015). In particular, two clades that are divergent but do not show pronounced phylogeographic structure were detected, confirming the great dispersal capacity of males of this high arctic species.
This dissertation thus represents a comprehensive investigation of Y-linked genetic variation on the intra- and interspecific level in a non-model organism. With my research, I contribute to an increased understanding of the complex evolutionary history of bears. In particular, I show that male-biased gene flow strongly influences the distribution of nuclear genetic variation, and that the contrast between phylogenies of differentially inherited markers can help to understand interspecific hybridization between closely related species. Moreover, my findings demonstrate the potential of Y-chromosomal markers to uncover unknown evolutionary patterns and processes. This applies not only to bears but to many species, even such that are generally well known and well described.
A great challenge in life sciences remains the site-specific modification of proteins with minimal perturbation for in vitro as well as in vivo studies. Therefore, different chemoselective reactions and semi-synthetic techniques such as native chemical ligation or intein-mediated protein splicing have been established. They enable a site-specific incorporation of chemical reporters into proteins, such as organic fluorophores or unnatural amino acids. In this PhD Thesis, protein trans-splicing was guided by minimal high-affinity interaction pairs to trace proteins in mammalian cells. In addition, the temporal modulation of cellular processes by photo-cleavable viral immune evasins was achieved.
Protein trans-splicing mediated by split inteins is a powerful technique for site-specific and 'traceless' protein modifications. Despite recent developments there is still an urgent need for ultra-small high-affinity intein tags for in vitro and in vivo approaches. So far, only a very few in-cell applications of protein trans-splicing are reported, all limited to C-terminal protein modifications. Here, a strategy for covalent N-terminal intein-mediated protein labeling at sub-nanomolar probe concentrations was developed. Combined with the minimalistic Ni-trisNTA/His-tag interaction pair, the affinity between the intein fragments was increased 50-fold (KD ~ 10 nM). Site-specific and efficient 'traceless' protein modification by high-affinity trans-splicing is demonstrated at nanomolar concentrations in mammalian cells.
High background originating from non-reacted, 'always-on' fluorescent probes still is a crucial issue in life sciences. Covalent labeling approaches with simultaneous activation of fluorescence are advantageous to increase sensitivity and to reduce background signal. Therefore, high-affinity protein trans-splicing was combined with fluorophore/quencher pairs for online detection of covalent N-terminal protein labeling in cellular environments. Substantial fluorescence enhancement at nanomolar probe concentrations was achieved. This ultra-small fluorogenic high-affinity split intein system is an unprecedented example for real-time monitoring of the trans-splicing reaction in cell-like environments as well as for protein labeling with fluorogenic probes at nanomolar concentrations.
To extend the field of chemical immunology and to address spatiotemporal aspects in adaptive immune response, new tools to control antigen processing are required. Therefore, synthetic photo-conditional viral immune evasins were designed to modulate antigen processing on demand. By using light, the time and dose controlled antigen translocation by the transporter associated with antigen processing (TAP) was triggered with response in the second regime. Peptide delivery and loading by the peptide-loading complex (PLC) was rendered inactive, whereas blocking was abolished in a light-controlled fashion to inactivate the synthetic viral immune evasin ICP47 along with simultaneous activation of the antigen presentation pathway. Lightresponsive peptide translocation by the TAP complex was assayed in vitro by utilizing microsomes isolated from professional antigen presenting B-cell lymphomas (Raji). To extend these studies, suppression and photo-controlled rescue of antigen presentation was examined at single-cell resolution in human primary immune cells.
Native chemical ligation interconnects peptide chemistry with recombinantly expressed proteins. This technique was applied to generate the semi-synthetic full-length ICP47. Although this approach was realized, the low product yield was not sufficient for further functional studies. Therefore, full-length ICP47 was consecutively generated by utilizing a full synthetic four-fragment ligation approach. However, this synthetic viral immune evasin was not able to block peptide translocation in a robust way.
Plastics contain a complex mixture of chemicals including polymers, additives, starting substances and side-products of processing. These plastic chemicals are prone to leach into the packaged goods, in the case of food contact materials (FCMs), or into the natural environment, in the case of plastic debris. Thus, plastics represent an exposure source of chemicals for humans and wildlife alike. While it is widely known that individual plastic chemicals, such as bisphenol A and phthalates, are hazardous, little is known on the overall chemical composition and toxicity of plastics. When fragmented into smaller particles, referred to as microplastics (< 5 mm), the plastic itself can be ingested by many species. It is well established that microplastic ingestion can have negative consequences for a wide range of organisms including invertebrates, but the contribution of plastic chemicals to the toxicity of microplastics is unclear.
Given the above, the present thesis aimed at a comprehensive toxicological, ecotoxicological and chemical characterization of everyday plastics. For a comparative evaluation, 77 plastic products were selected covering 16 material types (e.g., polyethylene) made from petroleum or renewable feedstocks. These products included biodegradable products, FCMs and non-FCMs, as well as raw materials and final products, respectively. In the first two studies, the chemical mixtures contained in the 77 products were extracted with methanol and extracts were analyzed in a set of four in vitro bioassays and by non-target high-resolution gas or liquid chromatography mass spectrometry. Since an exposure only occurs if chemicals actually leach under realistic conditions, in a third study migration experiments with water were conducted for 24 out of the 77 products. The aqueous migrates were assessed in the same way as the methanolic extracts. In addition, the freshwater invertebrate Daphnia magna was exposed chronically to microplastics made of polyvinylchloride (PVC), polyurethane (PUR) and polylactic acid (PLA) to investigate the contribution of chemicals in microplastic toxicity, in a fourth study.
The experimental findings demonstrate that a wide variety of chemicals is present in plastics. A single plastic product can contain up to several thousand chemical features, most of which unique to that product and at the same time unknown. The results also indicate that the majority of these chemical mixtures are toxic in vitro. Accordingly, 65% of the plastic extracts induced baseline toxicity and 42% an oxidative stress response, while 25% had an antiandrogenic and 6% an estrogenic activity. This implies that chemicals causing unspecific toxicity are more prevalent in plastics than such with endocrine effects. These chemicals can also leach from plastics under realistic conditions. Between 17 and 8936 chemical features were detected in a single migrate sample and all 24 tested migrates induced in vitro toxicity. This means that humans and wildlife can actually be exposed to toxic plastic chemicals under realistic conditions. Generally, each product has its individual toxicological and chemical fingerprint. Thus, neither material type, feedstock, biodegradability nor the food contact suitability of a product can serve as a predictor for the toxicity, the chemical composition or complexity of a product. Likewise, this means that bio-based and biodegradable materials are not superior to their petroleum-based counterparts from a toxicological perspective despite being promoted as sustainable alternatives to conventional plastics.
Moreover, the present thesis demonstrates that plastic chemicals can be the main driver for microplastic toxicity. Irregular microplastics made of PVC, PUR and PLA adversely affected life-history traits of D. magna in a polymer type- and endpoint-dependent manner at concentrations between 100 and 500 mg L-1 and with a higher efficiency than natural kaolin particles. While the toxicity of PVC was triggered by the chemicals used in the material, the effects of PUR and PLA were induced by the physical properties of the particle.
In addition, in the fifth study, results and observations made during this thesis were integrated inter- and transdisciplinarily with the perspectives of a social scientist and a product manufacturer. This elucidated that knowledge on plastic ingredients is often concealed, is lacking or not applicable in practice. These intransparencies hinder the safety evaluation of plastic products as well as the choice and sale of the least toxic packaging material.
Overall, the present thesis highlights that the chemical safety of plastics and their bio-based and biodegradable alternatives is currently not ensured. Thus, chemicals require more consideration in the toxicity and risk assessment of plastics and microplastics. Product-specific and complex chemical compositions, including unknown compounds, pose a challenge here. Two essential steps towards non-toxic products are to increase transparency along the product life cycle and to reduce the chemical complexity of plastics by communication and regulation. The results of the present thesis indicate that products exist which do not contain toxic chemicals. These can serve to direct the design of safer plastics. Since toxicity and chemical complexity seem to increase with processing, the integration of toxicity testing during the production steps would further support the safe and sustainable production and use of plastic products.
The increasing demand of the high value ω-3 fatty acids due to its beneficial role for human health, explains the huge need for alternative production ways of ω-3 fatty acids. The oleaginous alga Phaeodactylum tricornutum is a prominent candidate and has been investigated as biofactory for ω-3 fatty acids, e.g. the synthesis of eicosapentaenoic acid (EPA). In general, the growth and the lipid content of diatoms can be enhanced by genetic engineering or are influenced by environmental factors, e.g. nutrients, light or temperature.
In this study, the potential of P. tricornutum as biofactory was improved by heterologously expressing the hexose uptake protein 1 (HUP1) from the Chlorophyte Chlorella kessleri.
An in situ localization study revealed that only the full length HUP1 protein fused to eGFP was correctly targeted to the plasma membrane, whereas the N-terminal sequence of the protein is only sufficient to enter the ER. Protein and gene expression data displayed that the gene-promoter combination was relevant for the expression level of HUP1, while only cells expressing the protein under the light-inducible fcpA promoter showed a significant expression. In these mutants an efficient glucose uptake was detectable under mixotrophic growth condition, low light intensities and low glucose concentrations leading to an increased cell dry weight.
In a second approach, the growth and lipid content of wildtype cells were analyzed in a small 1l photobioreactor. Here, a commercial F/2 medium and a common culture medium, ASP and modified versions were compared. There was neither a significant impact on the growth and lipid content in P. tricornutum cells due to the supplemention of trace elements nor due to elevated salt concentrations in the media. In a modified version of ASP medium, with adapted nitrate and phosphate concentration a constantly high biomass productivity was achieved, yielding the highest value of 82 mg l-1 d-1 during the first three days. This was achieved even though light intensity was reduced by 40%. The differences in biomass productivity as well as the lipid content and the lipid composition underlined the importance of the choice of culture medium and the harvest time for enhanced growth and EPA yields in P. tricornutum.
Extreme convective precipitation events are among the most severe hazards in central Europe and are expected to intensify under global warming. However, the degree of intensification and the underlying processes are still uncertain. In this thesis, recent advances in continuous, radar-based precipitation monitoring and convection-permitting climate modeling are used to investigate Lagrangian properties of convective rain cells such as precipitation intensity, cell area, and precipitation sum and their relationship to large-scale, environmental conditions.
Firstly, convective precipitation objects are tracked in a gauge-adjusted radar-data set and the properties of these cells are related to large-scale environmental variables to investigate the observed super-Clausius-Clapeyron (CC) scaling of convective extreme precipitation. The Lagrangian precipitation sum of convective cells increases with dew point temperature at rates well above the CC-rate with increasing rates for higher dew point temperatures. These varying, high rates are caused by a covarying increase of CAPE with dew point temperature as well as the effect of high vertical wind shear causing an increase in cell area and thus precipitation sum. At the same time, cells move faster at high vertical wind shear so that Eulerian scaling rates are lower than Lagrangian but still above the CC-rate. The results show that wind shear and static instability need to be taken into account when transferring precipitation scaling under current climate conditions to future conditions. Secondly, the representation of convective cell properties in the convection-permitting climate model COSMO-CLM is evaluated. The model can simulate the observed frequency distributions of cell properties such as lifetime, area, mean and maximum intensity, and precipitation sum. The increase of area and intensity with lifetime is also well captured despite an underestimation of the intensity of the most severe cells. Furthermore, the model can represent the temperature scaling of intensity, area, and precipitation sum but fails to simulate the observed increase of lifetime. Thus, the model is suitable to study climatologies of convective storms in Germany. Thirdly, two COSMO-CLM projections at the end of the century under emission scenario RCP8.5 were investigated. While the number of convective cells and their lifetime remain approximately constant compared to present conditions, intensity and area increase strongly. The relative increase of intensity and area is largest for the highest percentiles meaning that extreme events intensify the most. The characteristic afternoon maximum of convective precipitation is damped, and shifted to later times of day which leads to an increase of nighttime precipitation in the future. Scaling rates of cell properties with dew point temperature are nearly identical in present and future in the simulation driven by the EC-Earth model which means that the upper limit of cell properties like intensity, area, and precipitation sum could be predicted from near-surface dew point temperature. However, this result could not be reproduced by the simulation driven by MIROC5 and needs further investigation.
Multidomain enzymes, such as fatty acid synthases (FASs) or polyketide synthases (PKSs), play a crucial role in the biosynthesis of important natural products. They have a high significance in the development of new pharmaceuticals and various research approaches focus on the engineering of these proteins. For example, human type I FAS is an interesting therapeutic target. Owing to its importance in lipogenesis, upregulation of human type I FAS expression has been observed in numerous cancers. Type I FAS is also regarded as important target in antiobesity treatment. Both multidomain enzyme classes - FASs and PKSs - show high structural and functional similarities. Particularly animal type I FAS is most relevant as evolutionary precursor of the PKS family. Therefore, the well characterized FASs are suitable model proteins for the poorly characterized PKSs, to gain deeper understanding in these megasynthases.
Furthermore, fatty acids are considered to be strategically important platform chemicals accessible through sustainable microbial approaches. The recently acquired structural information on FASs provides an excellent understanding of the molecular basis of fatty acid synthesis. The specific understanding of chain-length control, the characterization of a multitude of substrate-specific thioesterases, and the emerging tools and means for metabolic engineering have fostered targeted approaches for modulating chain length. There is large interest in short-chain fatty acids, since these compounds are biotechnologically valuable platform chemicals and biofuel precursors, and attempts on the synthesis of short-chain fatty acids have been reported during the last years.
Primary focus of this thesis lies on the animal type I FASs, which exhibit large conformational variety, as seen in electron microscopy and high-speed atomic force microscopy. Conformational dynamics facilitate productive protein-protein interactions between catalytic domains within the enzyme and aid acyl carrier protein (ACP)-mediated substrate shuttling during the catalytic cycle of fatty acid biosynthesis. To gain deeper insight into the fundamental processes of ACP-mediated substrate shuttling and the underlying conformational dynamics, spectroscopic methods like Förster resonance energy transfer and electron paramagnetic resonance spectroscopy shall be employed. These spectroscopic methods demand site-specific labeling of proteins with fluorophore or spin labels, which can be accomplished with the amber codon suppression technology. Through amber codon suppression, a non-canonical amino acid (ncAA) with an orthogonal functional group is incorporated site-specifically into the protein sequence, which can be used in chemoselective reactions for protein labeling.
This thesis is at the forefront of employing the technology of amber codon suppression for addressing complex biological questions on megasynthases. The successful production of ncAA-modified FASs is challenging. With the aim of incorporating ncAAs into the multidomain 540 kDa large murine FAS, we by far exceed boundaries of documented application of amber codon suppression. Most of the proteins that are reported by Liu & Schultz in applications of amber codon suppression are in the range of 30kDa - for example the TE domain of human FAS. In the same review, the largest protein amber codon suppression was applied to is a potassium channel with roughly 80 kDa. Thus, to the best of my knowledge no protein exceeding 100 kDa has been used in amber codon suppression so far.
In this thesis a low-complex, well-plate based reporter assay is presented, based on an ACP-GFP fusion protein for fast and efficient screening of ncAA incorporation. Reliability and applicability of the reporter assay is demonstrated by successful upscaling to larger protein constructs and increased expression scale.
As outlined in this thesis, we have carefully set up methods for the modification of murine FAS and made several achievements:
(i) We have created our own toolbox with a multitude of suppressor plasmids and various orthogonal pairs. pACU and pACE plasmids are compatible for fast exchange of cassettes, and cloning procedures are optimized for modification of synthetases by site-directed mutagenesis. (ii) We have organic synthesis of several ncAAs stably running in the lab and synthesis of other ncAAs can be established when required. Therefore, extensive screening at moderate costs is possible. (iii) We have established a reporter assay for screening our own library of vectors for amber codon suppression and for optimizing incorporation of ncAAs. (iv) We successfully incorporated ncAAs into subconstructs and full-length murine FAS, and collected initial promising results for the application of these proteins in spectroscopic methods. Thus, laying the foundation for future studies to address fundamental questions of the ACP-mediated substrate shuttling and other conformational dynamics of these enzymes.
This thesis contributes to the field of soft matter research and studies the importance of hydrodynamic interactions during free-solution electrophoresis of linear polyelectrolytes by means of coarse-grained molecular dynamics simulations including full electro-hydrodynamic interactions. The center of attention is the specific role of hydrodynamic interactions on the electrophoretic behaviour of charged macromolecules. Points of interest are the dependence of hydrodynamic interactions on the chain length, the chain flexibility and the surrounding counterions, and their combined influence on important observables such as the static chain conformations and the dynamic transport coefficients, i.e., the diffusion and the electrophoretic mobility. These problems are addressed by extensive computer simulations that are quantitatively matched with experimental results. Existing theoretical predictions are carefully examined and are augmented by the observations in this thesis.
HADES (High Acceptance DiElectron Spectrometer), located at GSI, is a versatile detector for precise spectroscopy of e+ e- pairs and charged hadrons produced on a fixed target in a 1 to 3.5 AGeV kinetic beam energy region. The main experimental goal is to investigate properties of dense nuclear matter created in heavy ion collisions and learn about in-medium hadron properties.
In the HADES set-up 24 Mini Drift Chambers (MDC) allow for track reconstruction and determining the particle momentum by exploiting charged particle deflection in a magnetic field. In addition, the drift chambers contribute to particle identification by measuring the energy loss. The read-out concept foresees each sensing wire to be equipped with a preamplifier, analog pulse shaper and discriminator. In the current front-end electronics, the ASD-8 ASIC comprises the above modules. Due to limitations of the current on-board time to digital converters (TDC), especially regarding higher reaction rates expected at the future FAIR facility (HADES at SIS-100), the electronics need to be replaced by new board featuring multi-hit TDCs. Whereas ASD-8 chips cannot be procured anymore, a promising replacement candidate is the PASTTREC ASIC, developed by JU Krakow, which was tested w.r.t. suitability for MDC read-out in a variety of set-ups and, where possible, in direct comparison to ASD-8.
The timing precision, being the most crucial performance parameter of the joint system of detector and read-out electronics, was assessed in two different set-ups, i.e. a cosmic muon tracking set-up and a beam test at the COSY accelerator at Juelich using a minimum ionizing proton beam.
The beam test results were reproduced and can thus be quantitatively explained in a three dimensional GARFIELD simulation of a HADES MDC drift cell. In particular, the simulation is able to describe the characteristic dependence of the time precision on the track position within the cell.
A circuit simulation (SPICE) was used to closely model the time development of a raw drift chamber pulse, measured as a response to X-rays from a 55 Fe source. The insights gained from this model were used for attributing realistic charge values to the time over threshold values measured with the read-out ASICs in a charge calibration set-up. Furthermore, a high-level circuit simulation of the PASTTREC shaper is implemented to serve as a demonstration of the effect of the individual shaping and tail cancellation stages which are present in both ASICs.