Fakultät für Geowissenschaften - Digitale Hochschulschriften der LMU

Ludwig-Maximilians-Universität München

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  1. 02/08/2016

    Entwicklung und Anwendung von Hochleistungs-Software für Mantelkonvektionssimulationen

    The Earth mantle convects on a global scale, coupling the stress field at every point to every other location at an instant. This way, any change in the buoyancy field has an immediate impact on the convection patterns worldwide. At the same time, mantle convection couples to processes at scales of a few kilometers or even a few hundred meters. Dynamic topography and the geoid are examples of such small-scale expressions of mantle convection. Also, the depth of phase transitions varies locally, with strong influences on the buoyancy, and thus the global stress field. In order to understand these processes dynamically it is essential to resolve the whole mantle at very high numerical resolutions. At the same time, geodynamicists are trying to answer new questions with their models, for example about the rheology of the mantle, which is most likely highly nonlinear. Also, due to the extremely long timescales we cannot observe past mantle states, which calls for simulations backwards in time. All these issues lead to an extreme demand in computing power. To cater to those needs, the physical models of the mantle have to be matched with efficient solvers and fast algorithms, such that we can efficiently exploit the enormous computing power of current and future high performance systems. Here, we first give an extensive overview over the physical models and introduce some numerical concepts to solve the equations. We present a new two-dimensional software as a testbed and elaborate on the implications of realistic mineralogic models for efficient mantle convection simulations. We find that phase transitions present a major challenge and suggest some procedures to incorporate them into mantle convection modeling. Then we give an introduction to the high-performance mantle convection prototype HHG, a multigrid-based software framework that scales to some of the fastest computers currently available. We adapt this framework to a spherical geometry and present first application examples to answer geodynamic questions. In particular, we show that a very thin and very weak asthenosphere is dynamically plausible and consistent with direct and indirect geological observations.

  2. 12/21/2015

    Molecular biology of octocoral mitochondria

    The mitochondria of non-bilaterian metazoans display a staggering diversity of genome organizations and also a slow rate of mtDNA evolution, unlike bilaterians, which may hold a key to understand the early evolution of the animal mitochondrion. Octocorals are unique members of Phylum Cnidaria, harboring several atypical mitochondrial genomic features, including a paucity of tRNA genes, various genome arrangements and the presence of novel putative mismatch repair gene (mtMutS) with various potential biological roles. Thus octocorals represents an interesting model for the study of mitochondrial biology and evolution. However, besides its utility in molecular phylogenetics, the mtDNA of octocorals is not studied from the perspective of DNA repair, oxidative stress response or gene expression; and there is a general lack of knowledge on the DNA repair capabilities and role of the mtMutS gene, response to climate-change, and mtDNA transcription in absence of interspersed tRNA genes of octocoral mitochondrial genome. In order to put the observed novelties in the octocoral mitochondria in an evolutionary and an environmental context, and to understand their potential functions and the consequences of their presence in conferring fitness during climate change induced stress, this study was undertaken. This dissertation aims to explore the uniqueness and diversity of octocoral mtDNA from an environmental as well as an evolutionary perspective. The thesis comprises five chapters exploring various facets of octocoral biology. The introductory section provides basic information and elaborates on the importance of studying non-bilaterian mitochondria. The first chapter sets the base for subsequent gene expression studies. Octocorals are extensively studied from a taxonomic and phylogenetic point of view. However, gene expression studies on these organisms have only recently started to appear. To successfully employ the most commonly used gene expression profiling technique i.e., the quantitation real-time PCR (qPCR), it is necessary to have an experimentally validated, treatment-specific set of stably expressed reference genes that will support for the accurate quantification of changes in expression of genes of interest. Hence, seven housekeeping genes, known to exhibit constitutive expression, were investigated for expression stability during simulated climate-changed (i.e. thermal and low-pH) induced stress. These genes were validated and subsequently used in gene expression studies on Sinularia cf. cruciata, our model octocoral. The occurrence of a mismatch repair gene, and the slow rates of mtDNA evolution in octocoral mitogenome calls for further investigations on the potential robustness of octocoral mitochondria to the increased oxidative stress. The second chapter presents a mitochondrion-centric view of climate-change stress response by investigating mtDNA damage, repair, and copy number dynamics during stress. The changes in gene expression of a set of stress-related nuclear, and mitochondrial genes in octocorals were also monitored. A robust response of octocoral mitochondria to oxidative mtDNA damage was observed, exhibiting a rapid recovery of the damaged mtDNA. The stress-specific regulation of the mtMutS gene was detected, indicating its potential involvement in stress response. The results highlight the resilience potential of octocoral mitochondria, and its adaptive benefits in changing oceans. The tRNA genes in animal mitochondria play a pivotal role in mt-mRNA processing and maturation. The influence of paucity of tRNA genes on transcription of the mitogenome in octocorals has not been investigated. The third chapter steps in the direction to understand the mitogenome transcription by investigating the nature of mature mRNAs. Several novel features not present in a “typical” animal mt-mRNAs were detected. The majority of the mitochondrial transcripts were observed as polycistronic units (i.e. the mRNA carrying information for the synthesis of more than one protein). 5’ and 3’ untranslated regions were delineated for most protein-coding genes. Alternative polyadenylation (APA) of mtMutS gene and long non-coding RNA (lncRNA) for ATP6 were detected and are reported for the first time in non-bilaterian metazoans providing a glimpse into the complexity and uniqueness of mtDNA transcription in octocorals. The mismatch repair (MMR) mechanism plays a crucial role in mutation avoidance and maintenance of genomic integrity. Its occurrence in animal mitochondria remains equivocal. Octocorals are the only known animals to posses an mtDNA-encoded MMR gene, the mtMutS, speculated to have self-contained DNA repair capability. In order to gain knowledge of the MMR activity in the octocoral mitochondria MMR assays using the octocoral mitochondrial fraction is necessary. A prerequisite for this assay is the availability of an MMR-substrate, which is a DNA fragment, usually a plasmid, containing the desired mismatch lesion (i.e. a heteroduplex) and a nicked strand. However, the methods to prepare such a substrate are time consuming and technically demanding. Chapter four describes two convenient and flexible strategies that can be used in parallel to prepare heteroduplex MMR substrate using a common plasmid and routine molecular biology techniques. This method should aid in MMR investigations in general, helping to advance this field of research. The mtMutS gene mentioned above is a bacterial homolog, predicted to have been horizontally transferred to the octocoral mitogenome. However, unlike the bacterial mutS, which is extensively studied, protein expression studies of the octocoral mtMutS gene are lacking. To investigate the biological role of the mtMutS protein, in vitro, and to gain knowledge on its structure and function, the expression of the gene in a bacterial host is necessary. The fifth chapter discusses the characteristics of the mtMutS protein, the efforts to express it in E. coli and some necessary precautions to be taken while working with the expression of such mtDNA-encoded proteins for the research in future. This dissertation elucidates and contributes to the understanding of the unexplored complexity of non-bilaterian mitochondria. It deals for the first time with DNA repair, gene expression and gene function, encompassing an integrative analysis of DNA, RNA and proteins to achieve its goals. This study forms the basis for many future investigations on the molecular mitochondrial biology of octocorals as well as other non-bilaterians, augmenting the understanding of the evolution of animal mitochondria, and also its role in cellular and organismal homeostasis in the context of environmental change.

  3. 11/04/2015

    An integrative approach using remote sensing and social analysis to identify different settlement types and the specific living conditions of its inhabitants

    Someday in 2007, the world population reached a historical landmark: for the first time in human history, more than half of the world´s population was urban. A stagnation of this urbanization process is not in sight, so that by 2050, already 70 percent of humankind is projected to live in urban settlements. Over the last few decades, enormous migrations from rural hinterlands to steadily growing cities could be witnessed coming along with a dramatic growth of the world’s urban population. The speed and the scale of this growth, particularly in the so called less developed regions, are posing tremendous challenges to the countries concerned as well as to the world community. Within mega cities the strongest trends and the most extreme dimensions of the urbanization process can be observed. Their rapid growth results in uncontrolled processes of fragmentation which is often associated with pronounced poverty, social inequality, socio-spatial and political fragmentation, environmental degradation as well as population demands that outstrip environmental service capacity. For the majority of the mega cities a tremendous increase of informal structures and processes has to be observed. Consequentially informal settlements are growing, which represent those characteristic municipal areas being subject to particularly high population density, dynamics as well as marginalization. They have quickly become the most visible expression of urban poverty in developing world cities. Due to the extreme dynamics, the high complexity and huge spatial dimension of mega cities, urban administrations often only have an obsolete or not even existing data basis available to be at all informed about developments, trends and dimensions of urban growth and change. The knowledge about the living conditions of the residents is correspondingly very limited, incomplete and not up to date. Traditional methods such as statistical and regional analyses or fieldwork are no longer capable to capture such urban process. New data sources and monitoring methodologies are required in order to provide an up to date information basis as well as planning strate¬gies to enable sustainable developments and to simplify planning processes in complex urban structures. This research shall seize the described problem and aims to make a contribution to the requirements of monitoring fast developing mega cities. Against this background a methodology is developed to compensate the lack of socio-economic data and to deduce meaningful information on the living conditions of the inhabitants of mega cities. Neither social science methods alone nor the exclusive analysis of remote sensing data can solve the problem of the poor quality and outdated data base. Conventional social science methods cannot cope with the enormous developments and the tremendous growth as they are too labor-, as well as too time- and too cost-intensive. On the other hand, the physical discipline of remote sensing does not allow for direct conclusions on social parameters out of remote sensing images. The prime objective of this research is therefore the development of an integrative approach − bridging remote sensing and social analysis – in order to derive useful information about the living conditions in this specific case of the mega city Delhi and its inhabitants. Hence, this work is established in the overlapping range of the research topics remote sensing, urban areas and social science. Delhi, as India’s fast growing capital, meanwhile with almost 25 million residents the second largest city of the world, represents a prime example of a mega city. Since the second half of the 20th century, Delhi has been transformed from a modest town with mainly administrative and trade-related functions to a complex metropolis with a steep socio-economic gradient. The quality and amount of administrative and socio-economic data are poor and the knowledge about the circumstances of Delhi’s residents is correspondingly insufficient and outdated. Delhi represents therefore a perfectly suited study area for this research. In order to gather information about the living conditions within the different settlement types a methodology was developed and conducted to analyze the urban environment of the mega city Delhi. To identify different settlement types within the urban area, regarding the complex and heterogeneous appearance of the Delhi area, a semi-automated, object-oriented classification approach, based on segmentation derived image objects, was implemented. As the complete conceptual framework of this research, the classification methodology was developed based on a smaller representative training area at first and applied to larger test sites within Delhi afterwards. The object-oriented classification of VHR satellite imagery of the QuickBird sensor allowed for the identification of five different urban land cover classes within the municipal area of Delhi. In the focus of the image analysis is yet the identification of different settlement types and amongst these of informal settlements in particular. The results presented within this study demonstrate, that, based on density classes, the developed methodology is suitable to identify different settlement types and to detect informal settlements which are mega urban risk areas and thus potential residential zones of vulnerable population groups. The remote sensing derived land cover maps form the foundation for the integrative analysis concept and deliver there¬fore the general basis for the derivation of social attributes out of remote sensing data. For this purpose settlement characteristics (e.g., area of the settlement, average building size, and number of houses) are estimated from the classified QuickBird data and used to derive spatial information about the population distribution. In a next step, the derived information is combined with in-situ information on socio-economic conditions (e.g., family size, mean water consumption per capita/family) extracted from georeferenced questionnaires conducted during two field trips in Delhi. This combined data is used to characterize a given settlement type in terms of specific population and water related variables (e.g., population density, total water consumption). With this integrative methodology a catalogue can be compiled, comprising the living conditions of Delhi’s inhabitants living in specific settlement structures – and this in a quick, large-scaled, cost effective, by random or regularly repeatable way with a relatively small required data basis.The combined application of remotely sensed imagery and socio-economic data allows for the mapping, capturing and characterizing the socio-economic structures and dynamics within the mega city of Delhi, as well as it establishes a basis for the monitoring of the mega city of Delhi or certain areas within the city respectively by remote sensing. The opportunity to capture the condition of a mega city and to monitor its development in general enables the persons in charge to identify unbeneficial trends and to intervene accordingly from an urban planning perspective and to countersteer against a non-adequate supply of the inhabitants of different urban districts, primarily of those of informal settlements. This study is understood to be a first step to the development of methods which will help to identify and understand the different forms, actors and processes of urbanization in mega cities. It could support a more proactive and sustainable urban planning and land management – which in turn will increase the importance of urban remote sensing techniques. In this regard, the most obvious and direct beneficiaries are on the one hand the governmental agencies and urban planners and on the other hand, and which is possibly the most important goal, the inhabitants of the affected areas, whose living conditions can be monitored and improved as required. Only if the urban monitoring is quickly, inexpensively and easily available, it will be accepted and applied by the authorities, which in turn enables for the poorest to get the support they need. All in all, the listed benefits are very convincing and corroborate the combined use of remotely sensed and socio-economic data in mega city research.

  4. 10/20/2015

    Genetic diversity of selected petrosiid sponges

    Sponges are simple animals that mostly inhabit the marine ecosystem. The role of sponges in the marine ecosystem and the potential of their bioactive compounds for the pharmaceutical industry have already been reviewed. Because of the extensive investigations of sponges within those two disciplines, marine ecology and chemistry, sponges are among the best-studied Metazoa. Likewise, sponges have been selected as animal models for investigating the origin of the multicellularity because sponges have a simple body structure and physiology (e.g., lack of nervous and circulatory organs). Due to their diversity and abundance in the tropics, particularly in the Indo-Pacific, sponges have also attracted taxonomists, systematists and ecologists to assess their diverseness and their phylogenetic and phylogeographic relationships. Resolving those research questions is difficult, because sponges are categorised as comparatively character poor taxa. By using only conservative taxonomy or systematics, the sponge diversity might therefore be underestimated. Inevitably, sponge biologists have to employ molecular methods as additional tools. In this research, molecular tools were used in order to analyse the taxonomy, phylogeny and phylogeographic relationships of selected sponge species. Xestospongia testudinaria & Neopetrosia exigua (Family Petrosiidae, Order Haplosclerida) were selected because of their conspicuousness in the Indo-Pacific coral reef ecosystems, whereby Xestospongia testudinaria is prominently known as the Indo-Pacific giant barrel sponge. Additionally, the order Haplosclerida has been described as an example of sponge order that has been examined systematically for a number of years and displays major discrepancy between morphology and molecular phylogenies. Molecular data suggests that the order needs revision at all taxonomic levels, which is the cause for further conflicts between taxonomists and systematists. In my research I focused mostly on sponge samples that originated from South East Asia or the Indo-Australian Archipelago (IAA). This region represents one of the best-explored marine regions in the Indo-Pacific. The aim of my research is to discover to what extent molecular tools are suitable to detect a phylogenetic signal, a phylogeographical break or a genotypic difference in the two selected sponge taxa. Several markers from the mitochondrial (mtDNA), ribosomal (rRNA) and nuclear (nucDNA) have been utilised. The 3' partition of the cytochrome oxidase subunit 1 (I3-M11 of cox1) from the mtDNA could be used to detect a genetic structure in Xestospongia testudinaria in a geographical narrow scale study of 200 km2 in Lembeh, North Sulawesi, Indonesia (Chapter 6) and throughout the Indo-Pacific despite limitations in the sample datasets (Chapter 2). In addition, the presence of a species complex in X. testudinaria was detected with the aid of phylogenetic reconstructions from a concatenation of mtDNA sequences (I3-M11 of cox1 and the Adenosine Triphosphate Synthase F0 subunit 6 / ATP6), and a nucDNA marker, the Adenosine Triphosphate Synthase β subunit intron (ATPS-β intron) (Chapter 6). At the same time, the presence of a species complex in X. testudinaria was recognised in a broader scale study of the Indo-Australian Archipleago (IAA) (Chapter 3). As a result, selected mtDNA and nucDNA markers in this thesis are useful for the investigation of the taxonomical status and phylogeographical relationships of X. testudinaria. A phylogeographical break in the IAA region due to the Pleistocene low sea level and Holocene recolonisation events (Chapter 3) could not be recovered among X. testudinaria in a phylogeographical analysis. Similarly, overlapping I3-M11 cox1 haplotypes between X. testudinaria, X. muta and X. bergquistia were recovered. This might be due to the presence of ancient polymorphisms on the barrel sponge mtDNA markers. Molecular tools are also used to help identifying my second selected sponge species (Chapter 4). The use of selected cox2 mtDNA and 28S rRNA markers contributed significantly to the identification of. Neopetrosia exigua used to be a congeneric of X. testudinaria. During my examinations of self-collected and holotype specimens I discovered that the species named N. exigua bears a wrong name. For this reason, a taxonomical revision is suggested and, more importantly, according to my findings and the principle of priority in the ICZN (International Code of Zoological Nomenclature) I use the species name ‘chaliniformis’ instead of the species name ‘exigua’. Furthermore, the use of selected nucDNA marker, the Lysidyl Aminoacyl Transfer RNA Synthetase (LTRS) intron, also contributes to the detection of phylogeographical breaks in N. chaliniformis of the IAA (Chapter 5). In a nutshell, the success of unravelling sponge taxonomies, phylogenies, and phylogeographic relationships always depends on the suitability of the utilised molecular markers and the significance of environmental influences on the sponges. Haplosclerid sponges possess limited morphological features. These hurdles create several problems, e.g. difficulties with taxa delimitation and unresolved phylogeography relationships. Even though the application of molecular techniques generated some limitations and obstacles in these studies, it has already contributed significantly to a better understanding of the phylogenies, phylogeographic relationships and taxonomical problems of X. testudinaria and N.chaliniformis, the species I selected for my research.

  5. 09/23/2015

    The life and death of heterogeneity in magmas

    Explosive volcanism is one of the most catastrophic material failure phenomena. During magma ascent, fragmentation produces particulate magma, which, if deposited above the glass transition of the interstitial melt, will sinter viscously. In-conduit tuffisites, conduit wall breccias and ash deposited from exceptionally hot pyroclastic flows are scenarios in which sintering by viscous flow is possible. Therefore, understanding the kinetics of sintering and the characteristic timescales over which magma densifies are critical to understanding the degassing timeframe in conduits and deposits. Viscous sintering is accompanied by a recovery of material strength towards that of a pore-free, dense magma. Understanding damage mechanisms and seismic behaviour prior to failure of sintered volcanic products are also crucial for the application of micromechanical models and material failure forecasting laws. Powdered standard glass and industrial glass beads have been used to explore sintering mechanisms at ambient pressure conditions and temporal evolution of connected and isolated pore-structure. I observe that sintering under low axial stress is essentially particle size, surface tension and melt viscosity controlled. I found that the timescales over which the bulk density approaches that of a pore-free melt at a given temperature is dependent on the particle-contact surface area, which can be estimated from the particle shape, the packing type and the initial total porosity. Granulometric constraint on the starting material indicates that the fraction of finer particles controls the rate of sintering as they cluster in pore spaces between larger particles and have a higher driving force for sintering due to their higher surface energy to volume ratio. Consequently, the resultant sample suite has a range of microstructures because the viscous sintering process promotes a fining of pores and a coarsening of particles. In a volcano, newly formed sintering material will then further contribute to magma-plugging of the conduit and its mechanical properties will affect magma rupture and its associated precursory signals. This consideration permitted me to explore the effect of sintering on the stress required for dynamic macroscopic failure of synthesised samples and assess the ability of precursory microseismic signals to be used as a failure forecast proxy at conditions relevant to shallow volcanic conduits. To this end, the samples were subjected to mechanical tests under a constant rate of deformation and at a temperature in the region of the material glass transition. A dual acoustic emission rig was employed to track the occurrence of brittle fracturing. The monitored acoustic dataset was then exploited to systematically assess the accuracy of the failure forecasting method as a function of heterogeneity (cast as porosity) since it acts as nucleating site for fracture propagation. The pore-emanating crack model describes well the peak stress at failure in the elastic regime for these materials. I show that the failure forecast method predicts failure within 0-15% error at porosities >0.2. However, when porosities are 100%. I interpret these results as a function of the low efficiency with which strain energy can be released in the scenario where there are few or no heterogeneities from which cracks can propagate. These observations shed light on questions surrounding the variable efficacy of the failure forecast method applied to active volcanoes. In particular, they provide a systematic demonstration of the fact that a good understanding of material properties is required. Thus I wish to emphasise the need for a better coupling of empirical failure forecasting models with mechanical parameters, such as failure criteria for heterogeneous materials, and point to the implications of this for a broad range of material-based disciplines.

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Die Universitätsbibliothek (UB) verfügt über ein umfangreiches Archiv an elektronischen Medien, das von Volltextsammlungen über Zeitungsarchive, Wörterbücher und Enzyklopädien bis hin zu ausführlichen Bibliographien und mehr als 1000 Datenbanken reicht. Auf iTunes U stellt die UB unter anderem eine Auswahl an Dissertationen der Doktorandinnen und Doktoranden an der LMU bereit.

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