Essays on consumption, insurance, and portfolio choice over the life cycle
Lorenz S. Schendel
- Die Dissertation besteht aus drei thematisch zusammenhängenden Forschungspapieren, in denen zeitstetige Konsum-, Investment- und Versicherungsprobleme über den Lebenszyklus betrachtet werden. Ein besonderer Fokus liegt auf realistischen Features wie stochastischem Sterberisiko und nicht-replizierbarem Einkommen. In der ersten Forschungsarbeit untersuche ich die Relevanz von stochastischem Sterberisiko. Dabei zeige ich, dass eine Sprungkomponente in der Sterberate die optimalen Entscheidungen der Agenten und das Wohlfahrtslevel signifikant beeinflusst. Eine Diffusionskomponente ist hingegen vernachlässigbar. In dem zweiten Forschungspapier untersuchen wir die Risikolebensversicherungsnachfrage einer Familie, dessen Alleinverdiener stochastischem Sterberisiko ausgesetzt ist. Wir achten insbesondere auf eine realistische Modellierung der Versicherung. Wir zeigen, dass dadurch junge Agenten dem Versicherungsmarkt fern bleiben und die Versicherungsnachfrage mit dem Alter steigt, im Gegensatz zu Modellen mit einfachen stetig-veränderbaren Versicherungen. Weiterhin verstärken langlaufende Versicherungsverträge die negativen Effekte von Einkommensschocks und werden daher von risikoaversen Agenten weniger abgeschlossen. In der dritten Forschungsarbeit untersuche ich die Critical Illness Versicherungsnachfrage eines Agenten in einem Modell mit stochastischem Sterberisiko und Gesundheitsausgaben. Die Versicherung übernimmt dabei die zusätzlichen Gesundheitskosten, die bei einem Sprung entstehen. Fast alle Agenten schließen solch eine Versicherung vor dem Rentenalter ab, selbst wenn diese sehr kostspielig ist. Insbesondere Agenten mit geringen Gesundheitsausgaben und hohem Einkommen haben eine hohe Versicherungsnachfrage.
Das Nukleon und sein chiraler Partner im Vakuum und in dichter Kernmaterie
- Kernpunkt dieser Arbeit ist die Untersuchung der Eigenschaften des Vakuums und des Grundzustandes von Kernmaterie anhand eines effektiven Modells. Das Lineare Sigma-Modell mit globaler chiraler U(2)R ×U(2)L-Symmetrie wurde mit (Axial-)Vektormesonen sowie dem chiralen Partner des Nukleons, der mit der Resonanz N(1535) identifiziert wird, erweitert. Die Einführung des chiralen Partners in der Spiegel-Zuordnung ermöglicht die Untersuchung zweier verschiedener Erzeugungsprozesse der Baryonenmasse: durch spontane Symmetriebrechung sowie durch einen chiral invarianten Massenterm, parametrisiert durch m0. Die Parameter des Modells werden durch experimentelle Werte der Zerfallsbreiten von N∗ → Nπ und a1 → πγ und der axialen Kopplungskonstante des Nukleons gN A , sowie durch Lattice-Berechnungen von gN∗ A fixiert. Im Rahmen dieses Modells ergibt sich für den Massenparameter m0 ∼ 500 MeV, was darauf hin deutet, dass ein beträchtlicher Anteil der Baryonenmasse nicht durch das chirale Kondensat erzeugt wird. Das Modell wird anhand des Zerfalls N∗ → Nη sowie s-Wellen-πN-Streulängen a(±) 0 validiert und zeigt gute Übereinstimmung mit dem Experiment. In Kernmaterie wird m0 durch Kondensate anderer skalarer Felder ausgedrückt, z. B. dem Tetraquark-Kondensat. Der Einfluß dieses Kondensates auf dichte Materie wird untersucht. Die Nukleonenmassen hängen stark von den Kondensaten ab und verschwinden, so wie auch die Kondensate selbst, wenn die chirale Symmetrie wieder hergestellt ist.
Function of flotillins in Alzheimer disease and apoptosis
Bincy Anu John
- Alzheimer’s disease (AD) is a common, age associated neurodegenerative disease that manifests as progressive dementia and is characterized by accumulation of the amyloid beta (Aβ) peptide which is a processing product of a transmembrane protein termed Alzheimer Amyloid Precursor Protein (APP). The Aβ peptide is generated by a sequential proteolytic processing of APP by two distinct proteases that are termed β- and γ-secretase. The β-secretase, also called BACE-1 or memapsin 2, belongs to the family of aspartyl proteases. BACE-1 evidently cleaves APP in an acidic endosomal compartment after endocytosis of APP, thereby facilitating Aβ peptide generation.
Sorting of transmembrane proteins is generally controlled by sorting signals in the cytoplasmic domains of the cargo proteins. The short cytoplasmic tail of BACE-1 with 23 amino acids contains a sorting signal of the acidic cluster, di-leucine (ACDL) type. The two Leu residues in this determinant are important for the clathrin mediated endocytosis of BACE-1, whereas the acidic residues together with the Leu are required for the endosomal sorting and recycling of BACE-1 back to the plasma membrane. The ACDL motif binds to the members of the GGA (Golgi-localized γ ear-containg ARF- binding proteins) family (GGA1-GGA3) that are involved in the sorting of BACE-1.
One of the major aims of this study was to address the role of flotillins in the intracellular sorting of BACE-1. This study shows that flotillin-1 directly binds to the di-leucine motif in the cytoplasmic tail of BACE-1, whereas flotillin-2 only shows an association mediated by flotillin-1. Flotillin-1 competes with GGA2 for the binding to BACE-1 tail, and thus influences the endosomal sorting of BACE-1. Importantly, depletion of flotillins results in an altered localization of the wildtype BACE-1, whereas the plasma membrane resident Leu to Ala (LLAA) mutant is not affected. Flotillin knockdown results in an accumulation of BACE-1, implicating reduced degradation and enhanced stability of this protease. Thus, flotillins appear to be important for the cellular targeting of BACE-1 and also influence the amyloidogenic processing of APP, as demonstrated by an increase in the amyloidogenic C-99 processing fragments.
When flotillin depleted cells were subjected to apoptotic stresses including Aβ25-35 synthetic peptide (inducer of the extrinsic apoptosis pathway) or several chemotherapeutic agents (staurosporine, brefeldin A, doxorubicin, carboplatin and paclitaxel: intrinsic apoptosis pathway) and cytotoxicity was determined, various apoptotic markers were activated in flotillin depleted cells. Caspase-3 and GGA3 are well accepted apoptosis markers and an enhanced caspase-3 cleavage was detected upon STS induced apoptosis in SH-SY5Y, HeLa, and HaCaT cell lines and increased GGA3 cleavage was observed in MCF7 cell line.
One of the major reasons for the apoptotic sensitivity in the absence of flotillins was a PI3K/Akt signaling defect. Neuroblastoma cells depleted of flotillins showed diminished levels of total Akt, phospho-Akt and phospho-ERK upon STS induced apoptosis. Since PI3K/Akt was the primary survival pathway affected upon STS induced apoptosis, ectopic expression of Akt in neuroblastoma cell line reduced caspase-3 cleavage and retarded apoptosis.
The direct downstream target of Akt is FOXO3a, whose localization was investigated in flotillin depleted cells. A major proportion of FOXO3a was localized in the nucleus of flotillin knockdown cells, implicating that FOXOs are active in these cells and subsequently trigger the transcription of death genes. Strikingly, an essential anti-apoptotic molecule and a major cancer target, Mcl-1, was inherently downregulated in flotillin knockdown cells. Mcl-1 is a chief member of the Bcl-2 family as it plays a pivotal role in cell survival and it is a critical protein in cancer therapeutics as suppression of Mcl-1 protein can curtail the survival and growth of tumorous cells.
Neuroblastoma cells were rescued from undergoing permanent damage due to STS induced apoptosis by overexpression of anti-apoptotic Bcl-2. Phorbol esters are well known PKC activators, and pre-treatment of neuroblastoma cells with phorbol esters along with staurosporine reduced caspase-3 cleavage.
These results demonstrate that absence of flotillins can sensitize cellular systems to apoptosis induction. The two main characteristics of cancer cells include resistance to apoptosis and unresponsiveness to chemotherapeutic agents. It is a well established fact that impaired apoptosis is central to tumour development. This study implicates that the downregulation of flotillin function can trigger cellular susceptibility and enhances apoptosis in response to conventional chemotherapeutic agents. Therefore, flotillins can serve as vital regulators in providing a more rational approach in molecular-targeted therapies for receding cancer growth and survival.
MALDI-MS characterization of the human 5-lipoxygenase protein
- 5-lipoxygenase (5-LO) is an enzyme with a substantial role in inflammatory processes. In vitro kinase assays using [32P]-ATP in combination with mutagenesis have revealed that serine residues 271, 523 and 663 can be phosphorylated by MK2, PKA and ERK2 kinases, respectively. A few available reports regarding 5-LO protein sequence have covered up to 30% of the sequence after amino acid sequencing including Ser663. In LCMS/MS analyses of 5-LO tryptic digests from different cellular sources different peptides have been detected; however, none of the three phosphorylations has been detected and only Ser663 was included in the covered sequence.
As there was no comprehensive mass spectrometric analysis of 5-LO, the purpose of this study was to optimize the experimental conditions under which detection of the aforementioned phosphorylation events, as well as other possible post-translational modifications (PTMs), would be feasible. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) was used for peptide analysis of 5-LO cleaved either by chemical reagents or by proteases. Sequence coverage of 5-LO could be enhanced to be close to completion by combination of results from digestions by trypsin, AspN and chymotrypsin. In-gel trypsin digestion followed by in-solution AspN digestion proved to be a useful sample treatment for reproducible detection of the Ser271-containing peptide.
Nevertheless, in none of the examined cleavage protocols the sequence around Ser523 was detected reproducibly or with acceptable signal intensity for subsequent peptide fragmentation. Propionic anhydride and sulfo-NHS-SS-biotin cross-linker (EZ-linkTM), were used for derivatization of lysine side chains and hindrance of lysine residue recognition by trypsin. Phosphopeptide enrichment became possible after tryptic digestion of these samples, not only due to formation of an individual Ser523-containing peptide, but also because TiO2-mediated enrichment, which is performed in acidic pH, was not impaired by positively charged free lysine side chains. Additionally, biotinylation of lysine residues was exploited for an intermediate enrichment step of the lysine containing peptides, prior to TiO2 phosphopeptide enrichment.
MALDI-MS analysis after in-vitro phosphorylation of 5-LO by the three kinases showed that Ser271 was phosphorylated in the MK2 and PKA kinase assays, while Ser523 was phosphorylated only in the PKA kinase assay. Surpisingly, no phosphopeptides were detected in the in-vitro kinase assays with ERK2, even though the unmodified counterpart of the Ser663-containing peptide was easily detected. The detection limit for each of the three phosphorylation sites was determined by the use of custom made phosphopeptides and an amount of 0.06 pmol of phosphopeptide in 1 μg 5-LO (representing 0.5% phosphorylation rate) was sufficient in all cases for successful enrichment and detection by MS.
In-vitro kinase assays with [32P]-ATP were performed for some kinases that were expected to phosphorylate 5-LO according to in-silico data. Three members of the Src tyrosine kinase family (Fgr, Hck and Yes) and the Ser/Thr specific kinase DNA-PK used 5-LO as their substrate and mainly residues at the N-terminal part of 5-LO were detected phosphorylated by MS (e.g. Y42, Y53). Additional in-vitro assays for recombinant 5-LO modification included incubation with glutathione or compound U73122, previously described as inhibitor of 5-LO.
Since in-vitro assays might have generated artifacts, a method for 5-LO purification from human cells was sought, in order to examine the modification state of the protein in the cellular context. ATP-agarose affinity purification and anti-5-LO immunoprecipitation proved inappropriate for sample purification for MALDI-MS analysis. Consequently, two human cell lines that are able to express 5-LO (Rec-1 Blymphocytes and MM6 monocytes) were transduced with a DNA cassette that contained recombinant human 5-LO sequence with an attached N-terminal FLAG-tag. Anti-FLAG immunoprecipitation was then performed effectively in cell lysates and the precipitated FLAG-5-LO was separated by SDS-PAGE before MALDI-MS analysis.
The examined cell stimuli were expected to result to phosphorylation of 5-LO at Ser523 by PKA in Rec-1 cells and to phosphorylation of Ser271 and/or Ser663 in MM6 cells by activated MK2 and ERK2, respectively. Additionally, under the conditions of MM6 cell stimulation, Fgr, Hck and Yes kinases, which phosphorylated 5-LO in vitro, were expected to be activated and the possibility of 5-LO phosphorylation on tyrosine was investigated. Although immunoblotting results indicated that all the aforementioned phosphorylation events existed in the examined samples, MALDI-MS analysis verified only phosphorylation on Ser271 in differentiated MM6 cells, interestingly regardless of cell stimulation.
Finally, the primary amine derivatization procedure by EZ-linkTM was utilized for MS analysis of lysine rich proteins. In the past, chemical propionylation of histones had been employed prior to trypsin digestion; however it was easily confused in MS with combinations of other PTMs (e.g. acetylation, methylation). Moreover, propionylation is a PTM for histone H3 and this information was lost. Consequently, the EZ-link reagent was more useful for analysis of histones, as unambiguous assignment of PTMs and detection of native propionylation on bovine H3 became possible.
Tribal gaming : stammeseigene Glücksspielunternehmen als Instrument kultureller, gesellschaftlicher und politischer Revitalisierung der indigenen Bevölkerung in den USA
- Die vorliegende Arbeit befasst sich mit der gegenwärtigen Situation der indigenen Bevölkerung in den Vereinigten Staaten von Amerika. Dort erleben viele Indianerstämme in jüngster Zeit einen nie dagewesenen wirtschaftlichen Aufschwung, der ihre bis dato äußerst ärmlichen Lebensverhältnisse grundlegend verbessert. Vor etwas mehr als zwei Jahrzehnten trat ein Gesetz in Kraft, das es den Stämmen gestattete, relativ unbehindert von einzelstaatlichen Restriktionen und Steuerbelastungen innerhalb ihrer Reservationsgebiete Glücksspiele für nichtindianische Besucher zu veranstalten. Seither haben sowohl Anzahl wie auch Gewinne der stammeseigenen Spielbetriebe in einem Maße zugenommen, das alle anfänglichen Erwartungen längst übertroffen hat. Tribal Gaming (oft auch Indian Gaming) ist zwar ein noch relativ rezentes Phänomen, doch es kann bereits jetzt festgestellt werden, dass es seit dem Beginn der europäischen Dominanz in Nordamerika keine Wirtschaftsstrategie gegeben hat, aus der so viele Indianerstämme gleichzeitig einen derart großen finanziellen Nutzen ziehen konnten. Für viele – wenn auch bei weitem nicht für alle – Indianerstämme ist das Kasino oder die Bingohalle inzwischen zur Haupteinnahmequelle geworden.
Die Untersuchung konzentriert sich auf die Auswirkungen dieses fundamentalen Wandels auf die indianischen Gemeinschaften insbesondere unter dem Gesichtspunkt der kulturellen und gesellschaftlichen Erneuerung und im weiteren Kontext auch auf ihre veränderte Rolle als Akteure im politischen System der USA. Im Mittelpunkt stehen also weniger die wirtschaftlichen Aspekte, als vielmehr die Frage, welchen Beitrag die stammeseigenen Glücksspielunternehmen als Instrument zur kulturellen, gesellschaftlichen und politischen Revitalisierung der indigenen Gesellschaften leisten können...
Are environmental conditions predisposing to calcium-deficiency rickets in developing countries? : A community-based case study from rural Kaduna, northern Nigeria
- Calcium-deficiency rickets (CDR) is a metabolic bone disease in children that is characterized by impaired mineralization and severe bone deformities. As CDR is often an endemic phenomenon that is almost exclusively restricted to tropical areas, environmental conditions are currently considered to be a possible predisposing factor for the CDR. Apart from a lack of macronutrients and micronutrients, an oversupply of potentially toxic elements (PTEs) in the soil-plant pathway of the CDR areas is thought to be involved in the aetiology of CDR. This study is the first to comprehensively analyze the impact of the environment on Ca deficiency and the resulting CDR.
To analyze the impact of the environment on CDR in developing countries, a rural region near Kaduna City, northern Nigeria, was chosen as a study area. From this area, cases of CDR have been reported since the early 2000s with a prevalence rate of 5%. Within this study area, 11 study sites, including areas with a high CDR prevalence (HR), a low CDR prevalence (LR) and no CDR prevalence (NR), were visited. In these HR, LR and NR study sites, the bedrock was investigated and the types of parent materials were identified. Local farmers were interviewed to determine the type and intensity of the land use. The soil types were determined along toposequences. The soil textures as well as the clay mineral fractions were determined. The pH values were measured, and the contents of organic carbon (OC) were determined. The potential cation-exchange capacity (CECpot) and the base saturation (BS) were analyzed. Furthermore, the total and plant-available macronutrient, micronutrient and PTE concentrations were measured in the soils. The drinking water was analyzed for pH values and the concentrations of Ca, Se and F were measured. The maize was analyzed for the Ca, Mg, K and P, Se and phytic acid (PA) contents.
The field and laboratory analyses on the bedrock showed that the HR, LR and NR study sites near Kaduna City, northern Nigeria, were underlain by Older Granites. A direct link between the distribution of the bedrock, the parent materials and the prevalence of CDR was not found. Interviews with the local farmers showed that the land use in the Kaduna study area is dominated by the cultivation of cash crops and food crops. Field analyzes on the soil types in the Kaduna study area showed that the distribution of the soil types is highly dependent on the topography and the distribution of the parent materials. In near vicinity to the inselbergs, Lixisols had developed on grus slope deposits. In the lower pediment and plain positions, Acrisols had developed on grus slope deposits and pisolite slope deposits. In the upper plains, Plinthosols had developed on pisolite slope deposits and in the river valleys, Fluvisols had developed on river deposits. Such soil types and soil type distributions are typical for granite-underlain areas in the northern guinea savanna of West Africa. Similarly, the physical soil conditions were representative for the soils of the northern guinea savanna: sandy topsoils, clayey subsoils and relatively high contents of kaolinite clay minerals in the clay fractions. With regard to the geochemical composition, no significant difference was found between the soils of the Kaduna study area and the soils of other granite-underlain areas in West Africa. Only the concentrations of P were considerably low in the soils of the Kaduna study area. However, P deficiency is a typical phenomenon in West African savanna soils and is not restricted to CDR areas. The micronutrient concentrations in the soils were low, but not critically low. Laboratory analyses on the amounts of PTEs showed that compared to worldwide background levels and international critical limits the PTE concentrations were very low in the soils of the Kaduna study area. In the drinking water, neither a significant lack of macronutrients and micronutrients, nor a noticeable oversupply of PTEs was found. The maize in the HR, LR and NR study sites contained normal contents of Mg, K and P, low contents of Ca and Se as well as slightly elevated concentrations of PA compared to West African food composition tables. Comparisons between the mineral contents of traditional and modern maize cultivars showed that the traditional maize cultivars contained significantly higher contents of Ca and noticeably lower concentrations of PA than the modern maize cultivars.
A direct link between the environmental conditions and the CDR in the Kaduna study area was considered unlikely, as neither a statistically significant lack of macronutrients and micronutrients, nor a statistically significant oversupply of PTEs was found in the environment of this area. Instead, the results indicated that the nutrition rather than the environmental conditions that impacts the prevalence of CDR.
The reconstruction of evolutionary patterns from daphnia resting egg banks
- In this study I analysed past and recent Daphnia populations from Lake Constance and Greifensee. Herefore, I first established a set of microsatellite markers applicable to European Hyalodaphnia species (chapter 1). Primers were also identified for species specific fragment lengths. 32 markers were then available to characterize the resting egg banks of Daphnia galeata and D. hyalina. Chapter 2 presents the reconstruction of the taxonomic composition in these two ecologically different lakes. This part of my work shows that the eutrophication that occurred in both lakes in the mid of the last century has strongly influenced the Daphnia populations. In both lakes Daphnia galeata established and hybridized with the indigenous D. hyalina. Interspecific hybridization resulted in introgression on the mitochondrial and nuclear level. In chapter 3 resting eggs from the sediments of the 1960s, 1970s, 1980s, 1990s and 2000s were characterized with microsatellite markers. The aim was to specify the extent of interspecific hybridization and nuclear introgression assuming that the genetic exchange between both species has an impact on their adaptation to their habitat. In life history experiments D. galeata and D. galeata x hyalina clones hatched from different time periods showed significant differential responses to food quality. Therefore, the question had to be answered how the Daphnia resting egg bank and the planktonic population are connected. In chapter 4 hatching experiments were conducted to bridge this gap of scientific knowledge in the life cycle of cyclic parthenogenetic waterfleas. Only D. galeata individuals were able to establish a clonal lineage after maturity. All observed recombinant individuals did not reproduce at all or firstly went through another sexual phase of reproduction i.e. produced resting eggs. In order to compare the findings of chapter 4 with the taxon composition of the recent planktonic population of Daphnia in Lake Constance, samples were taken over one season (between May 2005 and September 2006). During the season, the taxonomic composition of Daphnia changes severely with D. galeata being most abundant during the warm season and D. hyalina in the cold season. Moreover, some individuals were detected, that did not follow this pattern. With mitochondrial analysis those individuals were identified as mitochondrial introgressants and processed to life history experiments. Significant differences in the somatic growth rate under different temperatures (5°C, 12.5°C and 20°C) were related to the origin of the mitochondrial genome rather than the nuclear taxonomic assignment of the individual.
The findings of this study show that all organisms exposed to rapid ecological changes and their microevolutionary reaction to those.
Entwicklung eines standardorientierten Situational Judgement Tests zur Erfassung professioneller pädagogischer Kompetenz
- Kompetenzen bezeichnen „erlernbare kontextspezifische Leistungsdispositionen, die sich funktional auf Situationen und Anforderungen in bestimmten Domänen beziehen“ (Klieme & Hartig, 2007, S. 17). Für den Bereich der Lehrerbildung wurden durch die Kultusministerkonferenz (2004) Standards für die Lehrerbildung: Bildungswissenschaften formuliert, die als Explikation professioneller pädagogischer Kompetenzen gelten können. Durch die Formulierung dieser Standards sieht sich die Lehrerbildung mit der Aufgabe konfrontiert, Studierende des Lehramts so auszubilden, dass die resultierenden Kompetenzen den genannten Standards genügen. Dies impliziert eine standard- und somit kompetenzorientierte Evaluation der Lehrerbildung. Bislang wird eine Evaluation der Lehrerbildung jedoch meist durch Selbsteinschätzungsverfahren umgesetzt – eine Methodik, die im Bereich der Kompetenzdiagnostik kritisch diskutiert wird (z. B. Nerdinger et al, 2008).
Der Situational Judgement Test als kompetenzdiagnostisches Instrumentarium weist die Vorteile situationsorientierter Verfahren auf und kann zusätzlich aufgrund der schriftlichen Darbietung problemlos auf große Stichproben angewandt werden. In der vorliegenden Studie wurde ein solcher Test entwickelt, um die professionelle pädagogische Kompetenz Lehramtsstudierender kontextnah und ökonomisch erfassen zu können. Die Studie hatte zum Ziel, den entwickelten standardorientierten Situational Judgement Test anhand verschiedener Außenkriterien konvergent und diskriminant zu validieren. Hierbei wurden konvergente Validitätsnachweise lediglich teilweise signifikant, wobei diskriminante Validitätsnachweise anhand des Studienfachs (Lehramtsstudium vs. Studium technisch-naturwissenschaftlicher Fächer) deutliche Signifikanzen und Effektstärken zeigten.
Cell-free expression of GPCRs: the endothelin system
- The human endothelin receptors, ETA and ETB, are two members of the G-protein coupled receptors family (GPCRs) and they are key players in cardiovascular regulation. The characterization of their functionality in vitro has been limited by the possibility to obtain high quality samples using conventional expression systems. The Cell-Free expression system is an alternative technique for the production of membrane protein as well as GPCRs and can overcome some of the limitations that are commonly encountered using an in vivo approach. Cell-Free expression protocols for the two receptors ETA and ETB have been optimized by implementing post- and co-translational association to lipid bilayers. The efficiency of the reconstitution or association to liposomes and nanodiscs has systematically been studied and the ligand binding properties of the two receptors have been analyzed using a set of different complementary techniques. In several different conditions a high affinity binding of the peptide ligand ET-1 to both endothelin receptors could be obtained and the highest activity values were detected in sample prepared using a co-translational approach in presence of nanodiscs. Furthermore, the characteristic differential binding pattern of selected agonists and antagonists to the two receptors was confirmed. In samples obtained from several Cell-Free expression conditions, two intrinsic properties of the functionally folded ETB receptor, such as the proteolytic processing based on conformational recognition as well as the formation of SDS-resistant complexes with the peptide ligand ET-1, were detected. ETA and ETB are able to induce in vivo the activation of hetrotrimeric G proteins upon stimulation with an agonist, leading to the dissociation of the heterotrimeric complex and the exchange of GDP to GTP in the Galpha subunit. The Cell-Free expression system was chosen for the production of two G alpha subunit, Galpha s and Galpha q. Soluble expression of the two proteins was achieved and the production of active Galpha s was confirmed using fluorescent as well as radioactive assays. In conclusion, the obtained results document a new process for the production of ligand binding competent endothelin receptors, as well as Galpha proteins, using a Cell-Free expression system. The combination of this expression system and the nanodiscs technology appears to be a promising tool for the further characterization of membrane proteins as well as GPCRs.
On development, feasibility, and limits of highly efficient CPU and GPU programs in several fields
- With processor clock speeds having stagnated, parallel computing architectures have achieved a breakthrough in recent years. Emerging many-core processors like graphics cards run hundreds of threads in parallel and vector instructions are experiencing a revival. Parallel processors with many independent but simple arithmetical logical units fail executing serial tasks efficiently. However, their sheer parallel processing power makes them predestined for parallel applications while the simple construction of their cores makes them unbeatably power efficient. Unfortunately, old programs cannot profit by simple recompilation. Adaptation often requires rethinking and modifying algorithms to make use of parallel execution. Many applications have some serial subroutines which are very hard to parallelize, hence contemporary compute clusters are often homogeneous, offering fast processors for serial tasks and parallel processors for parallel tasks. In order not to waste the available compute power, highly efficient programs are mandatory.
This thesis is about the development of fast algorithms and their implementations on modern CPUs and GPUs, about the maximum achievable efficiency with respect to peak performance and to power consumption respectively, and about feasibility and limits of programs for CPUs, GPUs, and heterogeneous systems. Three totally different applications from distinct fields, which were developed in the extent of this thesis, are presented.
The ALICE experiment at the LHC particle collider at CERN studies heavy-ion collisions at high rates of several hundred Hz, while every collision produces thousands of particles, whose trajectories must be reconstructed. For this purpose, ALICE track reconstruction and ALICE track merging have been adapted for GPUs and deployed on 64 GPU-enabled compute-nodes at CERN.
After a testing phase, the tracker ran in nonstop operation during 2012 providing full real-time track reconstruction. The tracker employs a multithreaded pipeline as well as asynchronous data transfer to ensure continuous GPU utilization and outperforms the fastest available CPUs by about a factor three.
The Linpack benchmark is the standard tool for ranking compute clusters. It solves a dense system of linear equations using primarily matrix multiplication facilitated by a routine called DGEMM. A heterogeneous GPU-enabled version of DGEMM and Linpack has been developed, which can utilize the CAL, CUDA, and OpenCL APIs as backend. Employing this implementation, the LOEWE-CSC cluster ranked place 22 in the November 2010 Top500 list of the fastest supercomputers, and the Sanam cluster achieved the second place in the November 2012 Green500 list of the most power efficient supercomputers. An elaborate lookahead algorithm, a pipeline, and asynchronous data transfer hide the serial CPU-bound tasks of Linpack behind DGEMM execution on the GPU reaching the highest efficiency on GPU-accelerated clusters.
Failure erasure codes enable failure tolerant storage of data and real-time failover, ensuring that in case of a hardware defect servers and even complete data centers remain operational. It is an absolute necessity for present-day computer infrastructure. The mathematical theory behind the codes involves matrix-computations in finite fields, which are not natively supported by modern processors and hence computationally very expensive. This thesis presents a novel scheme for fast encoding matrix generation and demonstrates a fast implementation for the encoding itself, which uses exclusively either integer or logical vector instructions. Depending on the scenario, it is always hitting different hard limits of the hardware: either the maximum attainable memory bandwidth, or the peak instruction throughput, or the PCI Express bandwidth limit when GPUs or FPGAs are used.
The thesis demonstrates that in most cases with respect to the available peak performance, GPU implementations can be as efficient as their CPU counterparts.
With respect to costs or power consumption, they are much more efficient. For this purpose, complex tasks must be split in serial as well as parallel parts and the execution must be pipelined such that the CPU bound tasks are hidden behind GPU execution. Few cases are identified where this is not possible due to PCI Express limitations or not reasonable because practical GPU languages are missing.