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Nanostructured inorganic materials are routinely synthesized by the use of templates. Depending on the synthesis conditions of the product material, either “soft” or “hard” templates can be applied. For sol-gel processes, usually “soft” templating techniques are employed, while “hard” templates are used for high temperature synthesis pathways. In classical templating approaches, the template has the unique role of structure directing agent, in the sense that it is not participating to the chemical formation of the resulting material. This work investigates a new templating pathway to nanostructured materials, where the template is also a reagent in the formation of the final material. This concept is described as “reactive templating” and opens a synthetic path toward materials which cannot be synthesised on a nanometre scale by classical templating approaches. Metal nitrides are such kind of materials. They are usually produced by the conversion of metals or metal oxides in ammonia flow at high temperature (T > 1000°C), which make the application of classical templating techniques difficult. Graphitic carbon nitride, g-C3N4, despite its fundamental and theoretical importance, is probably one of the most promising materials to complement carbon in material science and many efforts are put in the synthesis of this material. A simple polyaddition/elimination reaction path at high temperature (T = 550°C) allows the polymerisation of cyanamide toward graphitic carbon nitride solids. By hard templating, using nanostructured silica or aluminium oxide as nanotemplates, a variety of nanostructured graphitic carbon nitrides such as nanorods, nanotubes, meso- and macroporous powders could be obtained by nanocasting or nanocoating. Due to the special semi-conducting properties of the graphitic carbon nitride matrix, the nanostructured graphitic carbon nitrides show unexpected catalytic activity for the activation of benzene in Friedel-Crafts type reactions, making this material an interesting metal free catalyst. Furthermore, due to the chemical composition of g-C3N4 and the fact that it is totally decomposed at temperatures between 600°C and 800°C even under inert atmosphere, g-C3N4 was shown to be a good nitrogen donor for the synthesis of early transition metal nitrides at high temperatures. Thus using the nanostructured carbon nitrides as “reactive templates” or “nanoreactors”, various metal nitride nanostructures, such as nanoparticles and porous frameworks could be obtained at high temperature. In this approach the carbon nitride nanostructure played both the role of the nitrogen source and of the exotemplate, imprinting its size and shape to the resulting metal nitride nanostructure.
A series of 9,10-diarylanthracenes with various substituents at the ortho positions have been synthesised by palladium-catalysed cross-coupling reactions. Such compounds exhibit interesting physical properties and can be applied as molecular switches. Despite the high steric demand of the substituents, products were formed in moderate-to-good yields. In some cases, microwave conditions further improved yields. Bis-coupling afforded two isomers (syn and anti) that do not interconvert at room temperature. These products were easily separated and their relative stereochemistries were unequivocally assigned by NMR spectroscopy and X-ray analysis. The syn and anti isomers exhibit different physical properties (e.g., melting points and solubilities) and interconversion by rotation around the aryl-aryl axis commences at <100 °C for fluoro-substituted diarylanthracenes and at >300 °C for alkyl- or alkoxy-substituted diarylanthracenes. The reactions with singlet oxygen were studied separately and revealed different reactivities and reaction pathways. The yields and reactivities depend on the size and electronic nature of the substituents. The anti isomers form the same 9,10-endoperoxides as the syn species, occasionally accompanied by unexpected 1,4-endoperoxides as byproducts. Thermolysis of the endoperoxides exclusively yielded the syn isomers. The interesting rotation around the aryl-aryl axis allows the application of 9,10-diarylanthracenes as molecular switches, which are triggered by light and air under mild conditions. Finally, the oxygenation and thermolysis sequence provides a simple, synthetic access to a single stereoisomer (syn) from an unselective coupling step.
This work analyzes the saving and consumption behavior of agents faced with the possibility of unemployment in a dynamic and stochastic life cycle model. The intertemporal optimization is based on Dynamic Programming with a backward recursion algorithm. The implemented uncertainty is not based on income shocks as it is done in traditional life cycle models but uses Markov probabilities where the probability for the next employment status of the agent depends on the current status. The utility function used is a CRRA function (constant relative risk aversion), combined with a CES function (constant elasticity of substitution) and has several consumption goods, a subsistence level, money and a bequest function.
We present a general framework for integrating annotations from different tools and tag sets. When annotating corpora at multiple linguistic levels, annotators may use different expert tools for different phenomena or types of annotation. These tools employ different data models and accompanying approaches to visualization, and they produce different output formats. For the purposes of uniformly processing these outputs, we developed a pivot format called PAULA, along with converters to and from tool formats. Different annotations are not only integrated at the level of data format, but are also joined on the level of conceptual representation. For this purpose, we introduce OLiA, an ontology of linguistic annotations that mediates between alternative tag sets that cover the same class of linguistic phenomena. All components are integrated in the linguistic information system ANNIS : Annotation tool output is converted to the pivot format PAULA and read into a database where the data can be visualized, queried, and evaluated across multiple layers. For cross-tag set querying and statistical evaluation, ANNIS uses the ontology of linguistic annotations. Finally, ANNIS is also tied to a machine learning component for semiautomatic annotation.
This thesis provides a novel view on the early stage of crystallization utilizing calcium carbonate as a model system. Calcium carbonate is of great economical, scientific and ecological importance, because it is a major part of water hardness, the most abundant Biomineral and forms huge amounts of geological sediments thus binding large amounts of carbon dioxide. The primary experiments base on the evolution of supersaturation via slow addition of dilute calcium chloride solution into dilute carbonate buffer. The time-dependent measurement of the Ca2+ potential and concurrent pH = constant titration facilitate the calculation of the amount of calcium and carbonate ions bound in pre-nucleation stage clusters, which have never been detected experimentally so far, and in the new phase after nucleation, respectively. Analytical Ultracentrifugation independently proves the existence of pre-nucleation stage clusters, and shows that the clusters forming at pH = 9.00 have a proximately time-averaged size of altogether 70 calcium and carbonate ions. Both experiments show that pre-nucleation stage cluster formation can be described by means of equilibrium thermodynamics. Effectively, the cluster formation equilibrium is physico-chemically characterized by means of a multiple-binding equilibrium of calcium ions to a ‘lattice’ of carbonate ions. The evaluation gives GIBBS standard energy for the formation of calcium/carbonate ion pairs in clusters, which exhibits a maximal value of approximately 17.2 kJ mol^-1 at pH = 9.75 and relates to a minimal binding strength in clusters at this pH-value. Nucleated calcium carbonate particles are amorphous at first and subsequently become crystalline. At high binding strength in clusters, only calcite (the thermodynamically stable polymorph) is finally obtained, while with decreasing binding strength in clusters, vaterite (the thermodynamically least stable polymorph) and presumably aragonite (the thermodynamically intermediate stable polymorph) are obtained additionally. Concurrently, two different solubility products of nucleated amorphous calcium carbonate (ACC) are detected at low binding strength and high binding strength in clusters (ACC I 3.1EE-8 M^2, ACC II 3.8EE-8 M^2), respectively, indicating the precipitation of at least two different ACC species, while the clusters provide the precursor species of ACC. It is proximate that ACC I may relate to calcitic ACC –i.e. ACC exhibiting short range order similar to the long range order of calcite and that ACC II may relate to vateritic ACC, which will subsequently transform into the particular crystalline polymorph as discussed in the literature, respectively. Detailed analysis of nucleated particles forming at minimal binding strength in clusters (pH = 9.75) by means of SEM, TEM, WAXS and light microscopy shows that predominantly vaterite with traces of calcite forms. The crystalline particles of early stages are composed of nano-crystallites of approximately 5 to 10 nm size, respectively, which are aligned in high mutual order as in mesocrystals. The analyses of precipitation at pH = 9.75 in presence of additives –polyacrylic acid (pAA) as a model compound for scale inhibitors and peptides exhibiting calcium carbonate binding affinity as model compounds for crystal modifiers- shows that ACC I and ACC II are precipitated in parallel: pAA stabilizes ACC II particles against crystallization leading to their dissolution for the benefit of crystals that form from ACC I and exclusively calcite is finally obtained. Concurrently, the peptide additives analogously inhibit the formation of calcite and exclusively vaterite is finally obtained in case of one of the peptide additives. These findings show that classical nucleation theory is hardly applicable for the nucleation of calcium carbonate. The metastable system is stabilized remarkably due to cluster formation, while clusters forming by means of equilibrium thermodynamics are the nucleation relevant species and not ions. Most likely, the concept of cluster formation is a common phenomenon occurring during the precipitation of hardly soluble compounds as qualitatively shown for calcium oxalate and calcium phosphate. This finding is important for the fundamental understanding of crystallization and nucleation-inhibition and modification by additives with impact on materials of huge scientific and industrial importance as well as for better understanding of the mass transport in crystallization. It can provide a novel basis for simulation and modelling approaches. New mechanisms of scale formation in Bio- and Geomineralization and also in scale inhibition on the basis of the newly reported reaction channel need to be considered.
Background: For omics experiments, detailed characterisation of experimental material with respect to its genetic features, its cultivation history and its treatment history is a requirement for analyses by bioinformatics tools and for publication needs. Furthermore, meta-analysis of several experiments in systems biology based approaches make it necessary to store this information in a standardised manner, preferentially in relational databases. In the Golm Plant Database System, we devised a data management system based on a classical Laboratory Information Management System combined with web-based user interfaces for data entry and retrieval to collect this information in an academic environment.
Results: The database system contains modules representing the genetic features of the germplasm, the experimental conditions and the sampling details. In the germplasm module, genetically identical lines of biological material are generated by defined workflows, starting with the import workflow, followed by further workflows like genetic modification (transformation), vegetative or sexual reproduction. The latter workflows link lines and thus create pedigrees. For experiments, plant objects are generated from plant lines and united in so-called cultures, to which the cultivation conditions are linked. Materials and methods for each cultivation step are stored in a separate ACCESS database of the plant cultivation unit. For all cultures and thus every plant object, each cultivation site and the culture's arrival time at a site are logged by a barcode-scanner based system. Thus, for each plant object, all site-related parameters, e. g. automatically logged climate data, are available. These life history data and genetic information for the plant objects are linked to analytical results by the sampling module, which links sample components to plant object identifiers. This workflow uses controlled vocabulary for organs and treatments. Unique names generated by the system and barcode labels facilitate identification and management of the material. Web pages are provided as user interfaces to facilitate maintaining the system in an environment with many desktop computers and a rapidly changing user community. Web based search tools are the basis for joint use of the material by all researchers of the institute.
Conclusion: The Golm Plant Database system, which is based on a relational database, collects the genetic and environmental information on plant material during its production or experimental use at the Max-Planck-Institute of Molecular Plant Physiology. It thus provides information according to the MIAME standard for the component 'Sample' in a highly standardised format. The Plant Database system thus facilitates collaborative work and allows efficient queries in data analysis for systems biology research.
A woman and a language
(2008)
a- vs. B-languages or 2nd position vs. verb-adjacent clitics in west andsouth slavic languages?
(2008)
A chemotaxonomic evaluation using hplc profiling was undertaken to resolve the infrageneric and intergeneric affinities of over 150 strains of Xylariaceae. Daldinia placentiformis, Hypoxylon nicaraguense, H. polyporus, and Phylacia sagrana were found to contain 8-methoxy-1-naphthol, which is apparently absent in Annulohypoxylon, Hypoxylon, and related genera with bipartite stromata. D. placentiformis and other species of Daldinia and Entonaema produced this naphthol, 5-hydroxy-2-methylchromone, isosclerone derivatives, and 'AB-5046' phytotoxins. Phylacia sagrana differed from most Daldinia spp., except for D. caldariorum, by producing eutypine derivatives in addition to the above compounds. indolylquinones were observed in H. nicaraguense and H. polyporus. Isosclerones were also identified in the A. multiforme complex, but Hypoxylon and other Annulohypoxylon and most Hypoxylon spp. studied Annulohypoxylon spp. contained S-methylmellein as the major metabolite of their cultures. Based on the occurrence of the above metabolites, further mellein-type dihydroisocoumarins, teleomorphic and anamorphic Xylariaceae with Nodulisporium-like anamorphs ('Hypoxyloideae') were divided into various chemotypes. A comparison of their 5.8S/ ITS nuc-rDNA sequences agreed in some important aspects with the above results: H. nicaraguense and H. polyporus appeared basal to a clade comprising Daldinia, Entonaema, and Ph. sagrana. The latter species appeared allied to D. caldariorum, but was distantly related to Pyrenomyxa morganii and Hypoxylon s. str. (C) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
This study investigated whether older adults could acquire the ability to perform 2 cognitive operations in parallel in a paradigm in which young adults had been shown to be able to do so (K. Oberauer & R. Kliegl, 2004). Twelve young and 12 older adults practiced a numerical and a visuospatial continuous memory updating task in single-task and dual-task conditions for 16 to 24 sessions. After practice, 9 young adults were able to process the 2 tasks without dual- task costs, but none of the older adults had reached the criterion of parallel processing. The results suggest a qualitative difference between young and older adults in how they approach dual-task situations.
Aliens, intregration
(2008)
Flood polders are part of the flood risk management strategy for many lowland rivers. They are used for the controlled storage of flood water so as to lower peak discharges of large floods. Consequently, the flood hazard in adjacent and downstream river reaches is decreased in the case of flood polder utilisation. Flood polders are usually dry storage reservoirs that are typically characterised by agricultural activities or other land use of low economic and ecological vulnerability. The objective of this thesis is to analyse hydraulic, environmental and economic impacts of the utilisation of flood polders in order to draw conclusions for their management. For this purpose, hydrodynamic and water quality modelling as well as an economic vulnerability assessment are employed in two study areas on the Middle Elbe River in Germany. One study area is an existing flood polder system on the tributary Havel, which was put into operation during the Elbe flood in summer 2002. The second study area is a planned flood polder, which is currently in the early planning stages. Furthermore, numerical models of different spatial dimensionality, ranging from zero- to two-dimensional, are applied in order to evaluate their suitability for hydrodynamic and water quality simulations of flood polders in regard to performance and modelling effort. The thesis concludes with overall recommendations on the management of flood polders, including operational schemes and land use. In view of future changes in flood frequency and further increasing values of private and public assets in flood-prone areas, flood polders may be effective and flexible technical flood protection measures that contribute to a successful flood risk management for large lowland rivers.
Although educational content in electronic form is increasing dramatically, its usage in an educational environment is poor, mainly due to the fact that there is too much of (unreliable) redundant, and not relevant information. Finding appropriate answers is a rather difficult task being reliant on the user filtering of the pertinent information from the noise. Turning knowledge bases like the online tele-TASK archive into useful educational resources requires identifying correct, reliable, and "machine-understandable" information, as well as developing simple but efficient search tools with the ability to reason over this information. Our vision is to create an E-Librarian Service, which is able to retrieve multimedia resources from a knowledge base in a more efficient way than by browsing through an index, or by using a simple keyword search. In our E-Librarian Service, the user can enter his question in a very simple and human way; in natural language (NL). Our premise is that more pertinent results would be retrieved if the search engine understood the sense of the user's query. The returned results are then logical consequences of an inference rather than of keyword matchings. Our E-Librarian Service does not return the answer to the user's question, but it retrieves the most pertinent document(s), in which the user finds the answer to his/her question. Among all the documents that have some common information with the user query, our E-Librarian Service identifies the most pertinent match(es), keeping in mind that the user expects an exhaustive answer while preferring a concise answer with only little or no information overhead. Also, our E-Librarian Service always proposes a solution to the user, even if the system concludes that there is no exhaustive answer. Our E-Librarian Service was implemented prototypically in three different educational tools. A first prototype is CHESt (Computer History Expert System); it has a knowledge base with 300 multimedia clips that cover the main events in computer history. A second prototype is MatES (Mathematics Expert System); it has a knowledge base with 115 clips that cover the topic of fractions in mathematics for secondary school w.r.t. the official school programme. All clips were recorded mainly by pupils. The third and most advanced prototype is the "Lecture Butler's E-Librarain Service"; it has a Web service interface to respect a service oriented architecture (SOA), and was developed in the context of the Web-University project at the Hasso-Plattner-Institute (HPI). Two major experiments in an educational environment - at the Lycée Technique Esch/Alzette in Luxembourg - were made to test the pertinence and reliability of our E-Librarian Service as a complement to traditional courses. The first experiment (in 2005) was made with CHESt in different classes, and covered a single lesson. The second experiment (in 2006) covered a period of 6 weeks of intensive use of MatES in one class. There was no classical mathematics lesson where the teacher gave explanations, but the students had to learn in an autonomous and exploratory way. They had to ask questions to the E-Librarian Service just the way they would if there was a human teacher.
Sf6 belongs to the Podoviridae family of temperate bacteriophages that infect gram-negative bacteria by insertion of their double-stranded DNA. They attach to their hosts specifically via their tailspike proteins. The 1.25 Å crystal structure of Shigella phage Sf6 tailspike protein (Sf6 TSP) reveals a conserved architecture with a central, right-handed ; helix. In the trimer of Sf6 TSP, the parallel ; helices form a left-handed, coiled;; coil with a pitch of 340 Å. The C-terminal domain consists of a ; sandwich reminiscent of viral capsid proteins. Further crystallographic and biochemical analyses show a Shigella cell wall O-antigen fragment to bind to an endorhamnosidase active site located between two ;-helix subunits each anchoring one catalytic carboxylate. The functionally and structurally related bacteriophage, P22 TSP, lacks sequence identity with Sf6 TSP and has its active sites on single subunits. Sf6 TSP may serve as an example for the evolution of different host specificities on a similar general architecture.
River reaches protected by dikes exhibit high damage potential due to strong value accumulation in the hinterland areas. While providing an efficient protection against low magnitude flood events, dikes may fail under the load of extreme water levels and long flood durations. Hazard and risk assessments for river reaches protected by dikes have not adequately considered the fluvial inundation processes up to now. Particularly, the processes of dike failures and their influence on the hinterland inundation and flood wave propagation lack comprehensive consideration. This study focuses on the development and application of a new modelling system which allows a comprehensive flood hazard assessment along diked river reaches under consideration of dike failures. The proposed Inundation Hazard Assessment Model (IHAM) represents a hybrid probabilistic-deterministic model. It comprises three models interactively coupled at runtime. These are: (1) 1D unsteady hydrodynamic model of river channel and floodplain flow between dikes, (2) probabilistic dike breach model which determines possible dike breach locations, breach widths and breach outflow discharges, and (3) 2D raster-based diffusion wave storage cell model of the hinterland areas behind the dikes. Due to the unsteady nature of the 1D and 2D coupled models, the dependence between hydraulic load at various locations along the reach is explicitly considered. The probabilistic dike breach model describes dike failures due to three failure mechanisms: overtopping, piping and slope instability caused by the seepage flow through the dike core (micro-instability). The 2D storage cell model driven by the breach outflow boundary conditions computes an extended spectrum of flood intensity indicators such as water depth, flow velocity, impulse, inundation duration and rate of water rise. IHAM is embedded in a Monte Carlo simulation in order to account for the natural variability of the flood generation processes reflected in the form of input hydrographs and for the randomness of dike failures given by breach locations, times and widths. The model was developed and tested on a ca. 91 km heavily diked river reach on the German part of the Elbe River between gauges Torgau and Vockerode. The reach is characterised by low slope and fairly flat extended hinterland areas. The scenario calculations for the developed synthetic input hydrographs for the main river and tributary were carried out for floods with return periods of T = 100, 200, 500, 1000 a. Based on the modelling results, probabilistic dike hazard maps could be generated that indicate the failure probability of each discretised dike section for every scenario magnitude. In the disaggregated display mode, the dike hazard maps indicate the failure probabilities for each considered breach mechanism. Besides the binary inundation patterns that indicate the probability of raster cells being inundated, IHAM generates probabilistic flood hazard maps. These maps display spatial patterns of the considered flood intensity indicators and their associated return periods. Finally, scenarios of polder deployment for the extreme floods with T = 200, 500, 1000 were simulated with IHAM. The developed IHAM simulation system represents a new scientific tool for studying fluvial inundation dynamics under extreme conditions incorporating effects of technical flood protection measures. With its major outputs in form of novel probabilistic inundation and dike hazard maps, the IHAM system has a high practical value for decision support in flood management.
In this paper we report the results of an elicited imitation task on dative case marking in non-canonical double object constructions with 22 German children (3;9-6;8). The aim was to test the proficiency of the children's grammar and to see which strategies they use to produce ditransitive sentences in which the direct object precedes the indirect object. The analysis of the children's utterances/imitations shows that the animacy of the direct object affects the overt dative case marking of the indirect object. Children made more errors repeating dative case marking when the direct object was inanimate, i.e., they produced the accusative case on the indirect object (non-adult-like). When both objects were animate, children correctly produced the dative case on the indirect object. We describe and account for these performance strategies of the children in the framework of Optimality Theory. Assuming that the same universal constraints are at work as in the adult grammar, the difference between adults and children lies in the constraint ranking. We focus on a prominent pattern found in children's performance, which is absent (or rather oppressed) in the corresponding adult performance, and show that one and the same grammar accounts for both (in the sense of "strong continuity"). (c) 2007 Elsevier B.V. All rights reserved.
The anisotropic effect of the planar nitrate anion NO3- has been ab initio calculated employing the Nucleus- Independent Chemical Shift (NICS) concept of von Ragué Schleyer and visualized as Iso-Chemical-Shielding Surfaces (ICSSs) of various (de)shieldings. Complexation-induced shifts in the 1H NMR spectra of nitrate/metal complexes or nitrate/receptor supramolecules can be separated now into anisotropic influences of the suitably coordinated nitrate anions and effects originating from differential sources.
Annual plants under cyclic disturbance regime : better understanding through model aggregation
(2008)
In their application for conservation ecology, 'classical' analytical models and individual-based simulation models (IBMs) both entail their specific strengths and weaknesses, either in providing a detailed and realistic representation of processes or in regard to a comprehensive model analysis. This well-known dilemma may be resolved by the combination of both approaches when tackling certain problems of conservation ecology. Following this idea, we present the complementary use of both an IBM and a matrix population model in a case study on grassland conservation management. First, we develop a spatially explicit IBM to simulate the long-term response of the annual plant Thlaspi perfoliatum (Brassicaceae), claspleaf pennycress, to different management schemes (annual mowing vs. infrequent rototilling) based on field experiments. In order to complement the simulation results by further analyses, we aggregate the IBM to a spatially nonexplicit deterministic matrix population model. Within the periodic environment created by management regimes, population dynamics are described by periodic products of annual transition matrices. Such periodic matrix products provide a very conclusive framework to study the responses of species to different management return intervals. Thus, using tools of matrix model analysis (e.g., loop analysis), we can both identify dormancy within the age-structured seed bank as the pivotal strategy for persistence under cyclic disturbance regimes and reveal crucial thresholds in some less certain parameters. Results of matrix model analyses are therefore successfully tested by comparing their results to the respective IBM simulations. Their implications for an enhanced scientific basis for management decisions are discussed as well as some general benefits and limitations of the use of aggregating modeling approaches in conservation.
Two sesquiterpenes, corymbolone and mustakone, isolated from the chloroform extract of the rhizomes of Cyperus articulatus, exhibited significant anti-plasmodial properties. Mustakone was approximately ten times more active than corymbolone against the sensitive strains of the Plasmodium falciparum.
The first application of a pnCCD detector for X-ray scattering experiments using white synchrotron radiation at BESSY II is presented. A Cd arachidate multilayer was investigated in reflection geometry within the energy range 7 keV < E < 35 keV. At fixed angle of incidence the two-dimensional diffraction pattern containing several multilayer Bragg peaks and respective diffuse-resonant Bragg sheets were observed. Since every pixel of the detector is able to determine the energy of every incoming photon with a resolution Delta E/E similar or equal to 10(-2). a three-dimensional dataset is finally obtained. In order to achieve this energy resolution the detector was operated in the so-called single-photon- counting mode. A full dataset was evaluated taking into account all photons recorded within 10(5) detector frames at a readout rate of 200 Hz. By representing the data in reciprocal-space coordinates, it becomes obvious that this experiment with the pnCCD detector provides the same information as that obtained by combining a large number of monochromatic scattering experiments using conventional area detectors.
Nested complementation plays an important role in expressing counter- i.e. star-free and first-order definable languages and their hierarchies. In addition, methods that compile phonological rules into finite-state networks use double-nested complementation or “double negation”. This paper reviews how the double-nested complementation extends to a relatively new operation, generalized restriction (GR), coined by the author (Yli-Jyrä and Koskenniemi 2004). This operation encapsulates a double-nested complementation and elimination of a concatenation marker, diamond, whose finite occurrences align concatenations in the arguments of the operation. The paper demonstrates that the GR operation has an interesting potential in expressing regular languages, various kinds of grammars, bimorphisms and relations. This motivates a further study of optimized implementation of the operator.
The uptake of nutrients and their subsequent chemical conversion by reactions which provide energy and building blocks for growth and propagation is a fundamental property of life. This property is termed metabolism. In the course of evolution life has been dependent on chemical reactions which generate molecules that are common and indispensable to all life forms. These molecules are the so-called primary metabolites. In addition, life has evolved highly diverse biochemical reactions. These reactions allow organisms to produce unique molecules, the so-called secondary metabolites, which provide a competitive advantage for survival. The sum of all metabolites produced by the complex network of reactions within an organism has since 1998 been called the metabolome. The size of the metabolome can only be estimated and may range from less than 1,000 metabolites in unicellular organisms to approximately 200,000 in the whole plant kingdom. In current biology, three additional types of molecules are thought to be important to the understanding of the phenomena of life: (1) the proteins, in other words the proteome, including enzymes which perform the metabolic reactions, (2) the ribonucleic acids (RNAs) which constitute the so-called transcriptome, and (3) all genes of the genome which are encoded within the double strands of desoxyribonucleic acid (DNA). Investigations of each of these molecular levels of life require analytical technologies which should best enable the comprehensive analysis of all proteins, RNAs, et cetera. At the beginning of this thesis such analytical technologies were available for DNA, RNA and proteins, but not for metabolites. Therefore, this thesis was dedicated to the implementation of the gas chromatography – mass spectrometry technology, in short GC-MS, for the in-parallel analysis of as many metabolites as possible. Today GC-MS is one of the most widely applied technologies and indispensable for the efficient profiling of primary metabolites. The main achievements and research topics of this work can be divided into technological advances and novel insights into the metabolic mechanisms which allow plants to cope with environmental stresses. Firstly, the GC-MS profiling technology has been highly automated and standardized. The major technological achievements were (1) substantial contributions to the development of automated and, within the limits of GC-MS, comprehensive chemical analysis, (2) contributions to the implementation of time of flight mass spectrometry for GC-MS based metabolite profiling, (3) the creation of a software platform for reproducible GC-MS data processing, named TagFinder, and (4) the establishment of an internationally coordinated library of mass spectra which allows the identification of metabolites in diverse and complex biological samples. In addition, the Golm Metabolome Database (GMD) has been initiated to harbor this library and to cope with the increasing amount of generated profiling data. This database makes publicly available all chemical information essential for GC-MS profiling and has been extended to a global resource of GC-MS based metabolite profiles. Querying the concentration changes of hundreds of known and yet non-identified metabolites has recently been enabled by uploading standardized, TagFinder-processed data. Long-term technological aims have been pursued with the central aims (1) to enhance the precision of absolute and relative quantification and (2) to enable the combined analysis of metabolite concentrations and metabolic flux. In contrast to concentrations which provide information on metabolite amounts, flux analysis provides information on the speed of biochemical reactions or reaction sequences, for example on the rate of CO2 conversion into metabolites. This conversion is an essential function of plants which is the basis of life on earth. Secondly, GC-MS based metabolite profiling technology has been continuously applied to advance plant stress physiology. These efforts have yielded a detailed description of and new functional insights into metabolic changes in response to high and low temperatures as well as common and divergent responses to salt stress among higher plants, such as Arabidopsis thaliana, Lotus japonicus and rice (Oryza sativa). Time course analysis after temperature stress and investigations into salt dosage responses indicated that metabolism changed in a gradual manner rather than by stepwise transitions between fixed states. In agreement with these observations, metabolite profiles of the model plant Lotus japonicus, when exposed to increased soil salinity, were demonstrated to have a highly predictive power for both NaCl accumulation and plant biomass. Thus, it may be possible to use GC-MS based metabolite profiling as a breeding tool to support the selection of individual plants that cope best with salt stress or other environmental challenges.
Modelling and empirical studies have shown that input from the regional seed pool is essential to maintain local species diversity. However, most of these studies have concentrated on simplified, if not neutral, model systems, and focus on a limited subset of species or on aggregated measures of diversity only (e.g., species richness or Shannon diversity). Thus they ignore more complex species interactions and important differences between species. To gain a better understanding of how seed immigration affects community structure at the local scale in real communities we conducted computer simulation experiments based on plant functional types (PFTs) for a species-rich, fire-prone Mediterranean-type shrubland in Western Australia. We developed a spatially explicit simulation model to explore the community dynamics of 38 PFTs, defined by seven traits - regeneration mode, seed production, seed size, maximum crown diameter, drought tolerance, dispersal mode and seed bank type - representing 78 woody species. Model parameterisation is based on published and unpublished data on the population dynamics of shrub species collected over 18 years. Simulation experiments are based on two contrasting seed immigration scenarios: (1) the 'equal seed input number' scenario, where the number of immigrant seeds is the same for all PFTs, and (2) the 'equal seed input mass' scenario, where the cumulative mass of migrating seeds is the same for all PFTs. Both scenarios were systematically tested and compared for different overall seed input values. Without immigration the local community drifts towards a state with only 13 coexisting PFTs. With increasing immigration rates in terms of overall mass of seeds the simulated number of coexisting PFTs and Shannon diversity quickly approaches values observed in the field. The equal seed mass scenario resulted in a more diverse community than did the seed number scenario. The model successfully approximates the frequency distributions (relative densities) of all individual plant traits except seed size for scenarios associated with equal seed input mass and high immigration rate. However, no scenario satisfactorily approximated the frequency distribution for all traits in combination. Our results show that regional seed input can explain the more aggregated measures of local community structure, and some, but not all, aspects of community composition. This points to the possible importance of other (untested) processes and traits (e.g., dispersal vectors) operating at the local scale. Our modelling framework can readily allow new factors to be systematically investigated, which is a major advantage compared to previous simulation studies, as it allows us to find structurally realistic models, which can address questions pertinent to ecological theory and to conservation management.
Assessing the risk of gene flow from genetically modified trees carrying mitigation transgenes
(2008)
This article describes a HMM-based word-alignment method that can selectively enforce a contiguity constraint. This method has a direct application in the extraction of a bilingual terminological lexicon from a parallel corpus, but can also be used as a preliminary step for the extraction of phrase pairs in a Phrase-Based Statistical Machine Translation system. Contiguous source words composing terms are aligned to contiguous target language words. The HMM is transformed into a Weighted Finite State Transducer (WFST) and contiguity constraints are enforced by specific multi-tape WFSTs. The proposed method is especially suited when basic linguistic resources (morphological analyzer, part-of-speech taggers and term extractors) are available for the source language only.
An der Universität Potsdam wird seit 2008 ein automatisiertes Verfahren angewandt, um Bruchparamter großer Erdbeben in quasi-Echtzeit, d.h. wenige Minuten nachdem sich das Beben ereignet hat, zu bestimmen und der Öffentlichkeit via Internet zur Verfügung zu stellen. Es ist vorgesehen, das System in das Deutsch-Indonesische Tsunamifrühwarnsystem (GITEWS) zu integrieren, für das es speziell konfiguriert ist. Wir bestimmen insbesondere die Dauer und die Ausdehnung des Erdbebens, sowie dessen Bruchgeschwindigkeit und -richtung. Dabei benutzen wir die Seismogramme der zuerst eintreffenden P Wellen vom Breitbandstationen in teleseimischer Entfernung vom Beben sowie herkömmliche Arrayverfahren in teilweise modifizierter Form. Die Semblance wir als Ähnlichkeitsmaß verwendet, um Seismogramme eines Stationsnetzes zu vergleichen. Im Falle eines Erdbebens ist die Semblance unter Berücksichtigung des Hypozentrums zur Herdzeit und während des Bruchvorgangs deutlich zeitlich und räumlich erhöht und konzentriert. Indem wir die Ergebnisse verschiedener Stationsnetzwerke kombinieren, erreichen wir Unabhängigkeit von der Herdcharakteristik und eine raum-zeitliche Auflösung, die es erlaubt die o.g. Parameter abzuleiten. In unserem Beitrag skizzieren wir die Methode. Anhand der beiden M8.0 Benkulu Erdbeben (Sumatra, Indonesien) vom 12.09.2007 und dem M8.0 Sichuan Ereignis (China) vom 12.05.2008 demonstrieren wir Auflösungsmöglichkeiten und vergleichen die Ergebnisse der automatisierten Echtzeitanwendung mit nachträglichen Berechnungen. Weiterhin stellen wir eine Internetseite zur Verfügung, die die Ergebnisse präsentiert und animiert. Diese kann z.B. in geowissenschaftlichen Einrichtungen an Computerterminals gezeigt werden. Die Internetauftritte haben die folgenden Adressen: http://www.geo.uni-potsdam.de/arbeitsgruppen/Geophysik_Seismologie/forschung/ruptrack/openday http://www.geo.uni-potsdam.de/arbeitsgruppen/Geophysik_Seismologie/forschung/ruptrack
We use seismic array methods (semblance analysis) to image areas of seismic energy release in the Sunda Arc region and world-wide. Broadband seismograms at teleseismic distances (30° ≤ Δ ≤ 100°) are compared at several subarrays. Semblance maps of different subarrays are multiplied. High semblance tracked over long time (10s of second to minutes) and long distances indicate locations of earthquakes. The method allows resolution of rupture characteristics important for tsunami early warning: start and duration, velocity and direction, length and area. The method has been successfully applied to recent and historic events (M>6.5) and is now operational in real time. Results are obtained shortly after source time, see http://www.geo.uni-potsdam.de/Forschung/Geophysik/GITEWS/tsunami.htm). Comparison of manual and automatic processing are in good agreement. Computational effort is small. Automatic results may be obtained within 15 - 20 minutes after event occurrence.
Being "in the game"
(2008)
When people describe themselves as being “in the game” this is often thought to mean they have a sense of presence, i.e. they feel like they are in the virtual environment (Brown/Cairns 2004). Presence research traditionally focuses on user experiences in virtual reality systems (e.g. head mounted displays, CAVE-like systems). In contrast, the experience of gaming is very different. Gamers willingly submit to the rules of the game, learn arbitrary relationships between the controls and the screen output, and take on the persona of their game character. Also whereas presence in VR systems is immediate, presence in gaming is gradual. Due to these differences, one can question the extent to which people feel present during gaming. A qualitative study was conducted to explore what gamers actually mean when they describe themselves as being “in the game.” Thirteen gamers were interviewed and the resulting grounded theory suggests being “in the game” does not necessarily mean presence (i.e. feeling like you are the character and present in the VE). Some people use this phrase just to emphasize their high involvement in the game. These findings differ with Brown and Cairns as they suggest at the highest state of immersion not everybody experiences presence. Furthermore, the experience of presence does not appear dependent on the game being in the first person perspective or the gamer being able to empathize with the character. Future research should investigate why some people experience presence and others do not. Possible explanations include: use of language, perception of presence, personality traits, and types of immersion.
Benefits of graphic design expertise in old age : compensatory effects of a graphical lexicon?
(2008)
In biological cells, the long-range intracellular traffic is powered by molecular motors which transport various cargos along microtubule filaments. The microtubules possess an intrinsic direction, having a 'plus' and a 'minus' end. Some molecular motors such as cytoplasmic dynein walk to the minus end, while others such as conventional kinesin walk to the plus end. Cells typically have an isopolar microtubule network. This is most pronounced in neuronal axons or fungal hyphae. In these long and thin tubular protrusions, the microtubules are arranged parallel to the tube axis with the minus ends pointing to the cell body and the plus ends pointing to the tip. In such a tubular compartment, transport by only one motor type leads to 'motor traffic jams'. Kinesin-driven cargos accumulate at the tip, while dynein-driven cargos accumulate near the cell body. We identify the relevant length scales and characterize the jamming behaviour in these tube geometries by using both Monte Carlo simulations and analytical calculations. A possible solution to this jamming problem is to transport cargos with a team of plus and a team of minus motors simultaneously, so that they can travel bidirectionally, as observed in cells. The presumably simplest mechanism for such bidirectional transport is provided by a 'tug-of-war' between the two motor teams which is governed by mechanical motor interactions only. We develop a stochastic tug-of-war model and study it with numerical and analytical calculations. We find a surprisingly complex cooperative motility behaviour. We compare our results to the available experimental data, which we reproduce qualitatively and quantitatively.
Bio-jETI
(2008)
Background: With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms for an LC/MS analysis of FAAH gene knockout.
Methods: Bio-jETI uses the jABC environment for service-oriented modeling and design as a graphical process modeling tool and the jETI service integration technology for remote tool execution.
Conclusions: As a service definition and provisioning platform, Bio-jETI has the potential to become a core technology in interdisciplinary service orchestration and technology transfer. Domain experts, like biologists not trained in computer science, directly define complex service orchestrations as process models and use efficient and complex bioinformatics tools in a simple and intuitive way.
Increasing production activities have been observed in many EU member states since the EU Commission sent a clear signal establishing and supporting the bioenergy industry. This article discusses current sector developments and therewith evolving biofuel value chain activities and management requirements by means of two German biofuel processing firms. Usually, the processing company can be regarded as the initiator of the regional value chains. In order to safeguard the high initial investments and secure efficient supply, the processing company relies on contract farming or profit participation rights rather than spot market interactions. In addition to discussing that point, this paper also explores opportunities and threats for the suppliers of raw materials as well as for the processors.
Bridehood revisited
(2008)
Background
Serotonin induces fluid secretion from Calliphora salivary glands by the parallel activation of the InsP3/Ca2+ and cAMP signaling pathways. We investigated whether cAMP affects 5-HT-induced Ca2+ signaling and InsP3-induced Ca2+ release from the endoplasmic reticulum (ER).
Results
Increasing intracellular cAMP level by bath application of forskolin, IBMX or cAMP in the continuous presence of threshold 5-HT concentrations converted oscillatory [Ca2+]i changes into a sustained increase. Intraluminal Ca2+ measurements in the ER of ß-escin-permeabilized glands with mag-fura-2 revealed that cAMP augmented InsP3-induced Ca2+ release in a concentration-dependent manner. This indicated that cAMP sensitized the InsP3 receptor Ca2+ channel for InsP3. By using cAMP analogs that activated either protein kinase A (PKA) or Epac and the application of PKA-inhibitors, we found that cAMP-induced augmentation of InsP3-induced Ca2+ release was mediated by PKA not by Epac. Recordings of the transepithelial potential of the glands suggested that cAMP sensitized the InsP3/Ca2+ signaling pathway for 5-HT, because IBMX potentiated Ca2+-dependent Cl- transport activated by a threshold 5-HT concentration.
Conclusion
This report shows, for the first time for an insect system, that cAMP can potentiate InsP3-induced Ca2+ release from the ER in a PKA-dependent manner, and that this crosstalk between cAMP and InsP3/Ca2+ signaling pathways enhances transepithelial electrolyte transport.
Caryl Phillips
(2008)
The modern foreland basin straddling the eastern margin of the Andean orogen is the prime example of a retro-arc foreland basin system adjacent to a subduction orogen. While widely studied in the central and southern Andes, the spatial and temporal evolution of the Cenozoic foreland basin system in the northern Andes has received considerably less attention. This is in part due to the complex geodynamic boundary conditions, such as the oblique subduction and accretion of the Caribbean plates to the already complex interaction between the Nazca and the South American plates. In the Colombian Andes, for example, a foreland basin system has been forming since ~80 Ma over an area previously affected by rift tectonics during the Mesozoic. This setting of Cenozoic contractile deformation superposed on continental crust pre-strained by extensional processes thus represents a natural, yet poorly studied experimental set-up, where the role of tectonic inheritance on the development of foreland basin systems can be evaluated. However, a detailed documentation of the early foreland basin evolution in this part of the Andes has thus far only been accomplished in the more internal sectors of the orogen. In this study, I integrate new structural, sedimentological and biostratigraphic data with low-temperature thermochronology from the eastern sector of the Colombian Andes, in order to provide the first comprehensive account of mountain building and related foreland basin sedimentation in this part of the orogen, and to assess as to what extent pre-existent basement anisotropies have conditioned the locus of foreland deformation in space and time. In the Medina Basin, along the eastern flank of the Eastern Cordillera, I integrated detailed structural mapping and new sedimentological data with a new chronostratigraphic framework based on detailed palynology that links an eastward-thinning early Oligocene to early Miocene syntectonic wedge containing rapid facies changes with an episode of fast tectonic subsidence starting at ~30 Ma. This record represents the first evidence of topographic loading generated by slip along the principal basement-bounding thrusts in the Eastern Cordillera to the west of the basin and thus constrains the onset of mountain building in this area. A comprehensive assessment of exhumation patterns based on zircon fission-track (ZFT), apatite fission-track (AFT) analysis and thermal modelling reveals the location of these thrust loads to have been located along the contractionally reactivated Soapaga Fault in the axial sector of the Eastern Cordillera. Farther to the east, AFT and ZFT data also document the onset of thrust-induced exhumation associated with contractional reactivation of the main range-bounding Servita Fault at ~20 Ma. Associated with this episode of orogenic growth, peak burial temperature estimates based on vitrinite reflectance data in the Cenozoic sedimentary record of the adjacent Medina Basin documents earlier incorporation of the western sector of the basin into the advancing fold and thrust belt. I combined these new thermochronological data with published AFT analyses and known chronologic indicators of brittle deformation in order to evaluate the patterns of orogenic-front migration in the Andes of central Colombia. This spatiotemporal analysis of deformation reveals an episodic pattern of eastward migration of the orogenic front at an average rate of 2.5-2.7 mm/yr during the Late Cretaceous-Cenozoic. I identified three major stages of orogen propagation. First, following initiation of mountain building in the Central Cordillera during the Late Cretaceous, the orogenic front propagate eastward at slow rates (0.5-3.1 mm/yr) until early Eocene times. Such slow orogenic advance would have resulted from limited accretionary flux related to slow and oblique (SW-NE-oriented) convergence of the Farallon and South American plates during that time. A second stage of rapid orogenic advance (4.0-18.0 mm/yr) during the middle-late Eocene, and locally of at least 100 mm/yr in the middle Eocene, resulted from initial tectonic inversion of the Eastern Cordillera. I correlate this episode of rapid orogen-front migration with an increase in the accretionary flux triggered by acceleration in convergence and a rotation of the convergence vector to a more orogen-perpendicular direction. Finally, stagnation of the Miocene deformation front along former rift-bounding reactivated faults in the eastern flank of the Eastern Cordillera led to a decrease in the rates of orogenic advance. Post-late Miocene-Pliocene thrusting along the actively deforming front of the Eastern Cordillera at this latitude suggests averaged Miocene-Holocene orogen propagation rates of 1.2-2.1 mm/yr. In addition, ZFT data suggest that exhumation along the eastern flank of the orogen occurred at moderate rates of ~0.3 mm/yr during the Miocene, prior to an acceleration of exhumation since the Pliocene, as suggested by recently published AFT data. In order to evaluate the relations between thrust loading and sedimentary facies evolution in the foreland, I analyzed gravel progradation in the foreland basin system. In particular, I compared one-dimensional Eocene to Pliocene sediment accumulation rates in the Medina basin with a three-dimensional sedimentary budget based on the interpretation of ~1800 km of industry-style seismic reflection profiles and borehole data tied to the new chronostratigraphic framework. The sedimentological data from the Medina Basin reveal rapid accumulation of fluvial and lacustrine sediments at rates of up to ~ 0.5 mm/yr during the Miocene. Provenance data based on gravel petrography and paleocurrents reveal that these Miocene fluvial systems were sourced by Upper Cretaceous and Paleocene sedimentary units exposed to the west, in the Eastern Cordillera. Peak sediment-accumulation rates in the upper Carbonera Formation and the Guayabo Group occur during episodes of gravel progradation in the proximal foredeep in the Early and Late Miocene. I interpreted this positive correlation between sediment accumulation and gravel deposition as the direct consequence of thrust activity in the Servita-Lengupá Fault. This contrasts with current models relating gravel progradation to episodes of tectonic quiescence in more distal portions of foreland basin systems and calls for a re-evaluation of tectonic history interpretations inferred from sedimentary units in other mountain belts. In summary, my results document a late Eocene-early Miocene eastward advance of the topographic loads associated with the leading edge of deformation in the northern Andes of Colombia. Crustal thickening of the Eastern Cordillera associated with initiation of thrusting along the Servitá Fault illustrates that this sector of the Andean orogen acquired ~90% of its present width already by the early Miocene (~20 Ma). My data thus demonstrate that inherited crustal anisotropies, such as the former rift-bounding faults of the Eastern Cordillera, favour a non-systematic progression of foreland basin deformation through time by preferentially concentrating accommodation of slip and thrust-loading. These new chronology of exhumation and deformation associated with specific structures in the Colombian Andes also constitutes an important advance towards the understanding of models for hydrocarbon maturation, migration and trap formation along the prolific petroleum province of the Llanos Basin in the modern foredeep area.
Chloroplasts as bioreactors : high-yield production of active bacteriolytic protein antibiotics
(2008)
Plants, more precisely their chloroplasts with their bacterial-like expression machinery inherited from their cyanobacterial ancestors, can potentially offer a cheap expression system for proteinaceous pharmaceuticals. This system would be easily scalable and provides appropriate safety due to chloroplasts maternal inheritance. In this work, it was shown that three phage lytic enzymes (Pal, Cpl-1 and PlyGBS) could be successfully expressed at very high levels and with high stability in tobacco chloroplasts. PlyGBS expression reached an amount of foreign protein accumulation (> 70% TSP) that has never been obtained before. Although the high expression levels of PlyGBS caused a pale green phenotype with retarded growth, presumably due to exhaustion of plastid protein synthesis capacity, development and seed production were not impaired under greenhouse conditions. Since Pal and Cpl-1 showed toxic effects when expressed in E. coli, a special plastid transformation vector (pTox) was constructed to allow DNA amplification in bacteria. The construction of the pTox transformation vector allowing a recombinase-mediated deletion of an E. coli transcription block in the chloroplast, leading to an increase of foreign protein accumulation to up to 40% of TSP for Pal and 20% of TSP for Cpl-1. High dose-dependent bactericidal efficiency was shown for all three plant-derived lytic enzymes using their pathogenic target bacteria S. pyogenes and S. pneumoniae. Confirmation of specificity was obtained for the endotoxic proteins Pal and Cpl-1 by application to E. coli cultures. These results establish tobacco chloroplasts as a new cost-efficient and convenient production platform for phage lytic enzymes and address the greatest obstacle for clinical application. The present study is the first report of lysin production in a non-bacterial system. The properties of chloroplast-produced lysins described in this work, their stability, high accumulation rate and biological activity make them highly attractive candidates for future antibiotics.
Choice-based Conjointanalyse
(2008)
Questions: 1. Are there differences among species in their preference for coniferous vs. deciduous forest? 2. Are tree and shrub species better colonizers of recent forest stands than herbaceous species? 3. Do colonization patterns of plant species groups depend on tree species composition? Location: Three deciduous and one coniferous recent forest areas in Brandenburg, NE Germany. Methods: In 34 and 21 transects in coniferous and deciduous stands, respectively, we studied the occurrence and percentage cover of vascular plants in a total of 150 plots in ancient stands, 315 in recent stands and 55 at the ecotone. Habitat preference, diaspore weight, generative dispersal potential and clonal extension were used to explain mechanisms of local migration. Regression analysis was conducted to test whether migration distance was related to species’ life-history traits. Results: 25 species were significantly associated with ancient stands and ten species were significantly more frequent in recent stands. Tree and shrub species were good colonizers of recent coniferous and deciduous stands. In the coniferous stands, all herbaceous species showed a strong dispersal limitation during colonization, whereas in the deciduous stands generalist species may have survived in the grasslands which were present prior to afforestation. Conclusions: The fast colonization of recent stands by trees and shrubs can be explained by their effective dispersal via wind and animals. This, and the comparably efficient migration of herbaceous forest specialists into recent coniferous stands, implies that the conversion of coniferous into deciduous stands adjacent to ancient deciduous forests is promising even without planting of trees.
In an area that contains high concentrations of natural organic matter, it is expected that it plays an important role on the behavior of rare earth elements (REE), like europium, and of trivalent actinides. Competitive interactions with H+, inorganic species, major cations, e.g. Ca(II) or Mg(II), could influence these metals transport and bioavailability. Competitive experiments between cations, which can bind differently to humic substances and Eu3+,will bring an improved understanding of the competitive mechanisms. The aim of this study is to acquire data for Eu(III)/Cu(II) and Eu(III)/Ca(II) competitive binding to a sedimentary originated humic acid (Gorleben, Germany). The NICA-Donnan parameters for Ca2+, Cu2+, and Eu3+ obtained from competitive binding experiments using Ca2+ or Cu2+ ion selective electrodes were used to model time-resolved laser fluorescence spectroscopy (TRLFS) measurements. Eu3+ and Cu2+ are in direct competition for the same type of sites,whereas Ca2+ has an indirect influence through electrostatic binding.
The study of biological interaction networks is a central theme in systems biology. Here, we investigate common as well as differentiating principles of molecular interaction networks associated with different levels of molecular organization. They include metabolic pathway maps, protein-protein interaction networks as well as kinase interaction networks. First, we present an integrated analysis of metabolic pathway maps and protein-protein interaction networks (PIN). It has long been established that successive enzymatic steps are often catalyzed by physically interacting proteins forming permanent or transient multi-enzyme complexes. Inspecting high-throughput PIN data, it has been shown recently that, indeed, enzymes involved in successive reactions are generally more likely to interact than other protein pairs. In this study, we expanded this line of research to include comparisons of the respective underlying network topologies as well as to investigate whether the spatial organization of enzyme interactions correlates with metabolic efficiency. Analyzing yeast data, we detected long-range correlations between shortest paths between proteins in both network types suggesting a mutual correspondence of both network architectures. We discovered that the organizing principles of physical interactions between metabolic enzymes differ from the general PIN of all proteins. While physical interactions between proteins are generally dissortative, enzyme interactions were observed to be assortative. Thus, enzymes frequently interact with other enzymes of similar rather than different degree. Enzymes carrying high flux loads are more likely to physically interact than enzymes with lower metabolic throughput. In particular, enzymes associated with catabolic pathways as well as enzymes involved in the biosynthesis of complex molecules were found to exhibit high degrees of physical clustering. Single proteins were identified that connect major components of the cellular metabolism and hence might be essential for the structural integrity of several biosynthetic systems. Besides metabolic aspects of PINs, we investigated the characteristic topological properties of protein interactions involved in signaling and regulatory functions mediated by kinase interactions. Characteristic topological differences between PINs associated with metabolism, and those describing phosphorylation networks were revealed and shown to reflect the different modes of biological operation of both network types. The construction of phosphorylation networks is based on the identification of specific kinase-target relations including the determination of the actual phosphorylation sites (P-sites). The computational prediction of P-sites as well as the identification of involved kinases still suffers from insufficient accuracies and specificities of the underlying prediction algorithms, and the experimental identification in a genome-scale manner is not (yet) doable. Computational prediction methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding P-sites. However the recognition of such motifs by the respective kinases is a spatial event. Therefore, we characterized the spatial distributions of amino acid residue types around P-sites and extracted signature 3D-profiles. We then tested the added value of spatial information on the prediction performance. When compared to sequence-only based predictors, a consistent performance gain was obtained. The availability of reliable training data of experimentally determined P-sites is critical for the development of computational prediction methods. As part of this thesis, we provide an assessment of false-positive rates of phosphoproteomic data.
Competition is a key process in plant populations and communities. We thus need, if we are to predict the responses of ecological systems to environmental change, a comprehensive and mechanistic understanding of plant competition. Considering competition, however, only at the population level is not sufficient because plant individuals usually are different, interact locally, and can adapt their behaviour to the current state of themselves and of their biotic and abiotic environment. Therefore, simulation models that are individual-based and spatially explicit are increasingly used for studying competition in plant systems. Many different individual-based modelling approaches exist to represent competition, but it is not clear how good they are in reflecting essential aspects of plant competition. We therefore first summarize current concepts and theories addressing plant competition. Then, we review individual-based approaches for modelling competition among plants. We distinguish between approaches that are used for more than 10 years and more recent ones. We identify three major gaps that need to be addressed more in the future: the effects of plants on their local environment, adaptive behaviour, and below-ground competition. To fill these gaps, the representation of plants and their interactions have to be more mechanistic than most existing approaches. Developing such new approaches is a challenge because they are likely to be more complex and to require more detailed knowledge and data on individual-level processes underlying competition. We thus need a more integrated research strategy for the future, where empirical and theoretical ecologists as well as computer scientists work together on formulating, implementing, parameterization, testing, comparing, and selecting the new approaches. (c) 2008 Rubel Foundation, ETH Zurich. Published by Elsevier GmbH. All rights reserved.
The complex formation of the ligands 1,12-diazaperylene (dap), 1,1-bisisoquinoline (bis), 2,2-bipyridine (bpy) and 1,10-phenanthroline (phen) with transition metal ions (M = Fe, Co, Ni, Cu, Zn, Ru, Os, Re, Pd, Pt, Ag and Cd) in the gas phase has been studied by electrospray ionization mass spectrometry. With the exception of Ru, Os, Fe, Ni and Cu, singly charged complexes [MLn]+ (n = 1,2) were observed. The complexes of dap and bis with Ru, Os, Fe and Ni ions, and the mixed ligand complexes with bpy and phen, are preferably of the doubly charged type [ML3]2+. In addition, collision- induced dissociation (CID) measurements were employed to evaluate the relative stabilities of these complexes. The CID experiments of mixed-ligand complexes which contain both dap and phen or dap and bpy exhibit preferential elimination of bpy, indicating that bpy is a weaker ligand than phen and dap.
Computational cosmology
(2008)
“Computational Cosmology” is the modeling of structure formation in the Universe by means of numerical simulations. These simulations can be considered as the only “experiment” to verify theories of the origin and evolution of the Universe. Over the last 30 years great progress has been made in the development of computer codes that model the evolution of dark matter (as well as gas physics) on cosmic scales and new research discipline has established itself. After a brief summary of cosmology we will introduce the concepts behind such simulations. We further present a novel computer code for numerical simulations of cosmic structure formation that utilizes adaptive grids to efficiently distribute the work and focus the computing power to regions of interests, respectively. In that regards we also investigate various (numerical) effects that influence the credibility of these simulations and elaborate on the procedure of how to setup their initial conditions. And as running a simulation is only the first step to modelling cosmological structure formation we additionally developed an object finder that maps the density field onto galaxies and galaxy clusters and hence provides the link to observations. Despite the generally accepted success of the cold dark matter cosmology the model still inhibits a number of deviations from observations. Moreover, none of the putative dark matter particle candidates have yet been detected. Utilizing both the novel simulation code and the halo finder we perform and analyse various simulations of cosmic structure formation investigating alternative cosmologies. These include warm (rather than cold) dark matter, features in the power spectrum of the primordial density perturbations caused by non-standard inflation theories, and even modified Newtonian dynamics. We compare these alternatives to the currently accepted standard model and highlight the limitations on both sides; while those alternatives may cure some of the woes of the standard model they also inhibit difficulties on their own. During the past decade simulation codes and computer hardware have advanced to such a stage where it became possible to resolve in detail the sub-halo populations of dark matter halos in a cosmological context. These results, coupled with the simultaneous increase in observational data have opened up a whole new window on the concordance cosmogony in the field that is now known as “Near-Field Cosmology”. We will present an in-depth study of the dynamics of subhaloes and the development of debris of tidally disrupted satellite galaxies.1 Here we postulate a new population of subhaloes that once passed close to the centre of their host and now reside in the outer regions of it. We further show that interactions between satellites inside the radius of their hosts may not be negliable. And the recovery of host properties from the distribution and properties of tidally induced debris material is not as straightforward as expected from simulations of individual satellites in (semi-)analytical host potentials.
The predictability of an upcoming word has been found to be a useful predictor in eye movement research, but is expensive to collect and subjective in nature. It would be desirable to have other predictors that are easier to collect and objective in nature if these predictors were capable of capturing the information stored in predictability. This paper contributes to this discussion by testing a possible predictor: conditional co-occurrence probability. This measure is a simple statistical representation of the relatedness of the current word to its context, based only on word co-occurrence patterns in data taken from the Internet. In the regression analyses, conditional co-occurrence probability acts like lexical frequency in predicting fixation durations, and its addition does not greatly improve the model fits. We conclude that readers do not seem to use the information contained within conditional co-occurrence probability during reading for meaning, and that similar simple measures of semantic relatedness are unlikely to be able to replace predictability as a predictor for fixation durations. Keywords: Co-occurrence probability, Cloze predictability, frequency, eye movement, fixation duration.
This first volume of the DIGAREC Series holds the proceedings of the conference “The Philosophy of Computer Games”, held at the University of Potsdam from May 8-10, 2008. The contributions of the conference address three fields of computer game research that are philosophically relevant and, likewise, to which philosophical reflection is crucial. These are: ethics and politics, the action-space of games, and the magic circle. All three topics are interlinked and constitute the paradigmatic object of computer games: Whereas the first describes computer games on the outside, looking at the cultural effects of games as well as on moral practices acted out with them, the second describes computer games on the inside, i.e. how they are constituted as a medium. The latter finally discusses the way in which a border between these two realms, games and non-games, persists or is already transgressed in respect to a general performativity.
We present an approach to the correlated dynamics of many-electron systems. We show, that the two-electron reduced density matrix (2RDM) can provide a suitable description of the real time evolution of a system. To achieve this, the hierarchy of equations of motion must be truncated in a practical way. Also, the computational effort, given that the 2RDM is represented by products of two-electron determinants, is discussed, and numerical model calculations are presented.
We present an approach to the correlated dynamics of many-electron systems. We show, that the twoelectron reduced density matrix (2RDM) can provide a suitable description of the real time evolution of a system. To achieve this, the hierarchy of equations of motion must be truncated in a practical way. Also, the computational effort, given that the 2RDM is represented by products of two-electron determinants, is discussed, and numerical model calculations are presented.
Bacteriophage HK620 infects Escherichia coli H and is closely related to Shigella phage Sf6 and Salmonella phage P22. All three Podoviridae recognize and cleave their respective host cell receptor polysaccharide by homotrimeric tailspike proteins. The three proteins exhibit high sequence identity in the 110 residues of their N-terminal particle- binding domains, but no apparent sequence similarity in their major, receptor-binding parts. We have biochemically characterized the receptor-binding part of HK620 tailspike and determined its crystal structure to 1.38 Å resolution. Its major domain is a right-handed parallel ;-helix, as in Sf6 and P22 tailspikes. HK620 tailspike has endo-N- acetylglucosaminidase activity and produces hexasaccharides of an O18A1-type O-antigen. As indicated by the structure of a hexasaccharide complex determined at 1.6 Å resolution, the endoglycosidase-active sites are located intramolecularly, as in P22, and not between subunits, as in Sf6 tailspike. In contrast, the extreme C-terminal domain of HK620 tailspike forms a ;-sandwich, as in Sf6 and unlike P22 tailspike. Despite the different folds, structure-based sequence alignments of the C-termini reveal motifs conserved between the three proteins. We propose that the tailspike genes of P22, Sf6 and HK620 have a common precursor and are not mosaics of unrelated gene fragments.
The crystal and molecular structures of trans-2,4,4-trimethyl-4-silathiane 1-oxide 1 and 4,4-dimethyl-4- silathiane 1,1-dioxide 2 were determined by single crystal X-ray diffraction. Both compounds have the chair conformation with the 2-Me and the S=O group in compound 1 occupying the equatorial positions. The DFT (B3LYP/6-311G(d,p)) and MP2 (MP2/6-311G(d,p)) theoretical calculations nicely reproduce the X-ray experimental geometry. The obtained results are discussed in connection with the electronic and structural properties of the compounds.
The spatial magnetic properties (Through Space NMR Shieldings - TSNMRS) of two cyclobutadiene derivatives (2 and 5) and of a number of cyclobutadiene dianion derivatives (3, 4 and 6-8) have been calculated by the GIAO perturbation method employing the Nucleus-Independent Chemical Shift (NICS) concept of P. v. Ragué Schleyer, and visualized as Iso-Chemical-Shielding Surfaces (ICSS) of various size and direction. TSNMRS values can be successfully employed to quantify and visualize the (anti)aromaticity of the compounds studied and to discuss the influence of Li+ complexation to cyclobutadiene dianion (4a, 7 and 8) on planar 4c,6e or three-dimensional 6c,6e aromaticity.