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Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types
(2021)
Background:
There is a huge body of scientific literature describing the relation between tumor types and anti-cancer drugs. The vast amount of scientific literature makes it impossible for researchers and physicians to extract all relevant information manually.
Methods:
In order to cope with the large amount of literature we applied an automated text mining approach to assess the relations between 30 most frequent cancer types and 270 anti-cancer drugs. We applied two different approaches, a classical text mining based on named entity recognition and an AI-based approach employing word embeddings. The consistency of literature mining results was validated with 3 independent methods: first, using data from FDA approvals, second, using experimentally measured IC-50 cell line data and third, using clinical patient survival data.
Results:
We demonstrated that the automated text mining was able to successfully assess the relation between cancer types and anti-cancer drugs. All validation methods showed a good correspondence between the results from literature mining and independent confirmatory approaches. The relation between most frequent cancer types and drugs employed for their treatment were visualized in a large heatmap. All results are accessible in an interactive web-based knowledge base using the following link: .
Conclusions:
Our approach is able to assess the relations between compounds and cancer types in an automated manner. Both, cancer types and compounds could be grouped into different clusters. Researchers can use the interactive knowledge base to inspect the presented results and follow their own research questions, for example the identification of novel indication areas for known drugs.
The concept that diversity promotes reliability of ecosystem function depends on the pattern that community-level biomass shows lower temporal variability than species-level biomasses. However, this pattern is not universal, as it relies on compensatory or independent species dynamics. When in contrast within--trophic level synchronization occurs, variability of community biomass will approach population-level variability. Current knowledge fails to integrate how species richness, functional distance between species, and the relative importance of predation and competition combine to drive synchronization at different trophic levels. Here we clarify these mechanisms. Intense competition promotes compensatory dynamics in prey, but predators may at the same time increasingly synchronize, under increasing species richness and functional similarity. In contrast, predators and prey both show perfect synchronization under strong top-down control, which is promoted by a combination of low functional distance and high net growth potential of predators. Under such conditions, community-level biomass variability peaks, with major negative consequences for reliability of ecosystem function.
1. Models aim to predict phytoplankton dynamics based on observed initial conditions and a set of equations and parameters. However, our knowledge about initial conditions in nature is never perfect. Thus, if phytoplankton dynamics are sensitive to small variations in initial conditions, they are difficult to predict. 2. We used time-series data from indoor mesocosm experiments with natural phyto- and zooplankton communities to quantify the extent to which small initial differences in the species, functional group and community biomass in parallel treatments were amplified or buffered over time. We compared the differences in dynamics between replicates and among all mesocosms of 1year. 3. Temperature-sensitive grazing during the exponential growth phase of phytoplankton caused divergence. In contrast, negative density dependence caused convergence. 4. Mean differences in biomass between replicates were similar for all hierarchical levels. This indicates that differences in their initial conditions were amplified to the same extent. Even though large differences in biomass occasionally occurred between replicates for a short time, dynamics returned to the same path at all hierarchical levels. This suggests that internal feedback mechanisms make the spring development of phytoplankton highly predictable.
Network analysis examines the role of species in ecological communities. The most common approach involves measurement of centrality of species or other groups of individuals based on their topological positions in food webs, followed by establishing the rank order of importance of these groups. However, ranking may differ considerably with indices of centrality and therefore comparison of rank orders is essential to obtain more meaningful results on species performance. Since ranking ignores absolute differences between centrality values, species orders may neglect important structural information in food webs. Consequently, simultaneous examination of the distribution of index values is inevitable. Hierarchical clustering and consensus generation revealed that rank orders of centrality exhibit a similar pattern over six example food webs, while distributions differ not only with indices because their relationships are largely inconsistent with food webs as well. Therefore, optimal analysis of networks and the selection of keystone species in any ecological study should rely upon both of these procedures. Similar conclusions are drawn from the detailed evaluation of a sample food web from the Florida Bay.
Kyub
(2019)
We present an interactive editing system for laser cutting called kyub. Kyub allows users to create models efficiently in 3D, which it then unfolds into the 2D plates laser cutters expect. Unlike earlier systems, such as FlatFitFab, kyub affords construction based on closed box structures, which allows users to turn very thin material, such as 4mm plywood, into objects capable of withstanding large forces, such as chairs users can actually sit on. To afford such sturdy construction, every kyub project begins with a simple finger-joint "boxel"-a structure we found to be capable of withstanding over 500kg of load. Users then extend their model by attaching additional boxels. Boxels merge automatically, resulting in larger, yet equally strong structures. While the concept of stacking boxels allows kyub to offer the strong affordance and ease of use of a voxel-based editor, boxels are not confined to a grid and readily combine with kuyb's various geometry deformation tools. In our technical evaluation, objects built with kyub withstood hundreds of kilograms of loads. In our user study, non-engineers rated the learnability of kyub 6.1/7.
Data obtained from foreign data sources often come with only superficial structural information, such as relation names and attribute names. Other types of metadata that are important for effective integration and meaningful querying of such data sets are missing. In particular, relationships among attributes, such as foreign keys, are crucial metadata for understanding the structure of an unknown database. The discovery of such relationships is difficult, because in principle for each pair of attributes in the database each pair of data values must be compared. A precondition for a foreign key is an inclusion dependency (IND) between the key and the foreign key attributes. We present with Spider an algorithm that efficiently finds all INDs in a given relational database. It leverages the sorting facilities of DBMS but performs the actual comparisons outside of the database to save computation. Spider analyzes very large databases up to an order of magnitude faster than previous approaches. We also evaluate in detail the effectiveness of several heuristics to reduce the number of necessary comparisons. Furthermore, we generalize Spider to find composite INDs covering multiple attributes, and partial INDs, which are true INDs for all but a certain number of values. This last type is particularly relevant when integrating dirty data as is often the case in the life sciences domain - our driving motivation.
Data dependencies, or integrity constraints, are used to improve the quality of a database schema, to optimize queries, and to ensure consistency in a database. In the last years conditional dependencies have been introduced to analyze and improve data quality. In short, a conditional dependency is a dependency with a limited scope defined by conditions over one or more attributes. Only the matching part of the instance must adhere to the dependency. In this paper we focus on conditional inclusion dependencies (CINDs). We generalize the definition of CINDs, distinguishing covering and completeness conditions. We present a new use case for such CINDs showing their value for solving complex data quality tasks. Further, we define quality measures for conditions inspired by precision and recall. We propose efficient algorithms that identify covering and completeness conditions conforming to given quality thresholds. Our algorithms choose not only the condition values but also the condition attributes automatically. Finally, we show that our approach efficiently provides meaningful and helpful results for our use case.
Data integration aims to combine data of different sources and to provide users with a unified view on these data. This task is as challenging as valuable. In this thesis we propose algorithms for dependency discovery to provide necessary information for data integration. We focus on inclusion dependencies (INDs) in general and a special form named conditional inclusion dependencies (CINDs): (i) INDs enable the discovery of structure in a given schema. (ii) INDs and CINDs support the discovery of cross-references or links between schemas. An IND “A in B” simply states that all values of attribute A are included in the set of values of attribute B. We propose an algorithm that discovers all inclusion dependencies in a relational data source. The challenge of this task is the complexity of testing all attribute pairs and further of comparing all of each attribute pair's values. The complexity of existing approaches depends on the number of attribute pairs, while ours depends only on the number of attributes. Thus, our algorithm enables to profile entirely unknown data sources with large schemas by discovering all INDs. Further, we provide an approach to extract foreign keys from the identified INDs. We extend our IND discovery algorithm to also find three special types of INDs: (i) Composite INDs, such as “AB in CD”, (ii) approximate INDs that allow a certain amount of values of A to be not included in B, and (iii) prefix and suffix INDs that represent special cross-references between schemas. Conditional inclusion dependencies are inclusion dependencies with a limited scope defined by conditions over several attributes. Only the matching part of the instance must adhere the dependency. We generalize the definition of CINDs distinguishing covering and completeness conditions and define quality measures for conditions. We propose efficient algorithms that identify covering and completeness conditions conforming to given quality thresholds. The challenge for this task is twofold: (i) Which (and how many) attributes should be used for the conditions? (ii) Which attribute values should be chosen for the conditions? Previous approaches rely on pre-selected condition attributes or can only discover conditions applying to quality thresholds of 100%. Our approaches were motivated by two application domains: data integration in the life sciences and link discovery for linked open data. We show the efficiency and the benefits of our approaches for use cases in these domains.
The reaction of oxygen-substituted naphthalenes with singlet oxygen (O-1(2)) has been investigated, and labile endoperoxides have been isolated and characterized at -78 degrees C for the first time. Low-temperature kinetics by UV spectroscopy revealed that alkoxy and silyloxy substituents remarkably increase the rate of photooxygenations compared to 1,4-dimethylnaphthalene, whereas acyloxy-substituted acenes are inert towards O-1(2). The reactivities nicely correlate with HOMO energies and free activation energies, which we determined by density functional theory calculations. The lability of the isolated endoperoxides is due to their very fast back reaction to the corresponding naphthalenes even at -20 degrees C under release of O-1(2), making them to superior sources of this reactive species under very mild conditions. Finally, a carbohydrate-substituted naphthalene has been synthesized, which reacts reversibly with O-1(2) and might be applied for enantioselective oxidations in future work.
The decomposition of anthracene endoperoxides has been investigated under various conditions. Thermolyses proceed via radical intermediates and afford anthracenes and rearrangement products, depending on the substitution pattern. Interestingly, not only the O-O but also the C-O bond can be cleaved homolytically. Under basic conditions fragmentations take place, affording anthraquinone, and reactive oxygen species. This mechanism explains the often observed decomposition of endoperoxides during work-up. Finally, an acid-catalyzed cleavage has been observed under release of hydrogen peroxide. The results should be interesting for the mechanistic understanding of peroxide decomposition and the endoperoxides might serve as mild sources of reactive oxygen species for future applications. Copyright (C) 2016 John Wiley & Sons, Ltd.
Stereoselective [4+2] Cycloaddition of Singlet Oxygen to Naphthalenes Controlled by Carbohydrates
(2021)
Stereoselective reactions of singlet oxygen are of current interest. Since enantioselective photooxygenations have not been realized efficiently, auxiliary control is an attractive alternative. However, the obtained peroxides are often too labile for isolation or further transformations into enantiomerically pure products. Herein, we describe the oxidation of naphthalenes by singlet oxygen, where the face selectivity is controlled by carbohydrates for the first time. The synthesis of the precursors is easily achieved starting from naphthoquinone and a protected glucose derivative in only two steps. Photooxygenations proceed smoothly at low temperature, and we detected the corresponding endoperoxides as sole products by NMR. They are labile and can thermally react back to the parent naphthalenes and singlet oxygen. However, we could isolate and characterize two enantiomerically pure peroxides, which are sufficiently stable at room temperature. An interesting influence of substituents on the stereoselectivities of the photooxygenations has been found, ranging from 51:49 to up to 91:9 dr (diastereomeric ratio). We explain this by a hindered rotation of the carbohydrate substituents, substantiated by a combination of NOESY measurements and theoretical calculations. Finally, we could transfer the chiral information from a pure endoperoxide to an epoxide, which was isolated after cleavage of the sugar chiral auxiliary in enantiomerically pure form.
Stereoselective [4+2] Cycloaddition of Singlet Oxygen to Naphthalenes Controlled by Carbohydrates
(2021)
Stereoselective reactions of singlet oxygen are of current interest. Since enantioselective photooxygenations have not been realized efficiently, auxiliary control is an attractive alternative. However, the obtained peroxides are often too labile for isolation or further transformations into enantiomerically pure products. Herein, we describe the oxidation of naphthalenes by singlet oxygen, where the face selectivity is controlled by carbohydrates for the first time. The synthesis of the precursors is easily achieved starting from naphthoquinone and a protected glucose derivative in only two steps. Photooxygenations proceed smoothly at low temperature, and we detected the corresponding endoperoxides as sole products by NMR. They are labile and can thermally react back to the parent naphthalenes and singlet oxygen. However, we could isolate and characterize two enantiomerically pure peroxides, which are sufficiently stable at room temperature. An interesting influence of substituents on the stereoselectivities of the photooxygenations has been found, ranging from 51:49 to up to 91:9 dr (diastereomeric ratio). We explain this by a hindered rotation of the carbohydrate substituents, substantiated by a combination of NOESY measurements and theoretical calculations. Finally, we could transfer the chiral information from a pure endoperoxide to an epoxide, which was isolated after cleavage of the sugar chiral auxiliary in enantiomerically pure form.
Seven enzymes have been screened for the cleavage of aryl acetates. Phenyl and naphthyl acetates react with lipases and esterases, whereas the sterically demanding anthracene acetate gave a conversion only with porcine liver esterase and esterase 2 from Bacillus subtilis (BS2). These two enzymes have been employed on a preparative (0.5 mmol) scale and afforded cleavage products in 91 and 94% yields, even for anthracene acetate. Thus, this method is superior to chemical cleavage with catalytic amounts of sodium methoxide (Zemplen conditions), which gave only low conversions. Finally, regioselectivity has been achieved with an anthracene bisacetate, in which an ethyl group controls the cleavage of the first acetate. This indicates that steric interactions play a crucial role in the enzymatic cleavage of aryl acetates, which might be interesting for future applications or the development of enzyme inhibitors.
Untersuchungen an neuartigen sauerstoffsubstituierten Donoren und Akzeptoren für Singulettsauerstoff
(2019)
Im Verlauf dieser Arbeit wurden Aromaten wie Naphthaline und Anthracene mit Singulettsauerstoff, einer reaktiven Form des gewöhnlichen Sauerstoffs, zu sogenannten Endoperoxiden umgesetzt. Die hier eingesetzten Systeme wurden mit funktionellen Gruppen modifiziert, die über eine Sauerstoffbrücke mit dem Aromaten verknüpft sind. Die daraus entstandenen Endoperoxide sind meist besonders labil und konnten in dieser Arbeit isoliert und umfassend untersucht werden.
Hierbei wurde zum einen das Reaktionsverhalten untersucht. Es konnte gezeigt werden, dass die Aromaten in Abhängigkeit ihrer funktionellen Gruppen unterschiedlich schnell mit Singulettsauerstoff reagieren. Die so ermittelten Reaktivitäten wurden zusätzlich durch theoretische Berechnungen gestützt.
Die resultierenden Endoperoxide wurden unter verschiedenen Bedingungen wie erhöhter Temperatur oder einem sauren bzw. basischen Milieu auf ihre Stabilität hin untersucht. Dabei konnte gezeigt werden, dass die auf Naphthalinen basierenden Endoperoxiden den gebundenen Singulettsauerstoff in guten Ausbeuten oft schon bei sehr niedrigen Temperaturen (−40 bis 0 °C) freisetzen. Diese Verbindungen können daher als milde Quellen dieser reaktiven Sauerstoffspezies eingesetzt werden. Weiterhin konnten bei den Anthracenendoperoxiden Zerfallsmechanismen aufgeklärt und andere reaktive Sauerstoffspezies wie Wasserstoffperoxid oder Persäuren nachgewiesen werden.
Zu den Modifikationen der Aromaten gehören auch Glucosereste. Dadurch könnten sich die hier hergestellten Endoperoxide als vielversprechende Verbindungen in der Krebstherapie herausstellen, da Krebszellen deutlich stärker als gesunde Zellen kohlenhydratreiche Verbindungen für ihren Stoffwechsel benötigen. Bei der Spaltung von Endoperoxiden mit Glucosesubstituenten werden ebenfalls reaktive Sauerstoffspezies frei, die so zum Zelltod führen könnten.
We demonstrate a tilted pulse-front transient grating (TG) technique that allows to optimally utilize time resolution as well as TG line density while probing under grazing incidence as typically done in extreme ultraviolet (EUV) or soft x-ray (SXR) experiments. Our optical setup adapts the pulse front tilt of the two pulses that create the TG to the grazing incident pulse. We demonstrate the technique using all 800 nm femtosecond laser pulses for TG generation on a vanadium dioxide film. We probe that grating via diffraction of a third 800 nm pulse. The time resolution of 90 fs is an improvement by a factor of 30 compared to our previous experiments on the same system. The scheme paves the way for EUV and SXR probing of optically induced TGs on any material.
Traditional economic theory could not explain, much less predict, the near collapse of the financial system and its long-lasting effects on the global economy. Since the 2008 crisis, there has been increasing interest in using ideas from complexity theory to make sense of economic and financial markets. Concepts, such as tipping points, networks, contagion, feedback, and resilience have entered the financial and regulatory lexicon, but actual use of complexity models and results remains at an early stage. Recent insights and techniques offer potential for better monitoring and management of highly interconnected economic and financial systems and, thus, may help anticipate and manage future crises.
Arthur Schopenhauer (1788–1860) was perhaps the last polymath among the great Germanic philosophers. Switching with ease and elegance between epistemic positions and fields as diverse as idealism and empiricism, fideism and rationalism, realism and nominalism, art and religion, jurisprudence and politics, psychology and occultism, Schopenhauer erected an imposing edifice bearing testimony to his universal learning. This study is an investigation into the very conclusion of Schopenhauer’s philosophy and endeavours to answer the following question: did Schopenhauer’s doctrine of salvation issue forth organically from his intellectual output or was it annexed to his philosophy as a result of his critical engagement with religion? The labyrinthine paths through which Schopenhauer arrives at the soteriological culmination of his philosophy are subjected to critical assessment; the picture that emerges is of a philosopher who seemed convinced that he had solved some of the most pressing cosmic riddles to have tormented mankind through the ages.
Aus dem Inhalt dieser Ausgabe: Artikel und Miszellen: Karl E. Grözinger: Manfred Voigts zum Sechzigsten - 2.5.2006 Caspar Battegay: Wie nicht erinnern? - Die Frage nach der Jüdischkeit in Heinrich Heines autobiographischen Texten Edith Lutz: Heinrich Heine im "Verein für Cultur und Wissenschaft der Juden" Jakob Hessing: Wahrheit und Dichtung - Die Damaskusaffäre und Heines Der Rabbi von Bacharach Elvira Grözinger: Im Venusberg. Zu Gesundheit und Krankheit bei Heinrich Heine zwischen Eros und Thanatos Sabine Bierwirth: Meilenstein der Zeitgeschichtsschreibung: Heinrich Heines Berichte über die Judenverfolgung in Damaskus 1840 Hans Otto Horch: Die unheilbar große Brüderkrankheit - Zum programmatischen Zeitgedicht Das neue Israelitische Hospital zu Hamburg von H. Heine Hendrik Madsen: Vom Überleben der toten Schrift - Eine medientheoretisch orientierte Lektüre des Jeremiabuches Manfred Voigts: Moses Mendelssohn und Franz Kafka: Die Heilige Schrift Olivia Franz-Klauser: Samaritanerforschung im 19. Jahrhundert: Die Anfänge der historischen Kritik im Schatten religiöser Vorurteile, gezeigt an der Rezeption Moritz Heidenheims (1824-1898) Rezensionen: Mark R. Cohen: Unter Kreuz und Halbmond. Die Juden im Mittelalter (Daniel Jütte) Erika Timm: Historische jiddische Semantik. (Karl E. Grözinger) David B. Ruderman, Giuseppe Veltri (Hrsg.): Cultural Intermediaries. Jewish Intellectuals in Early Modern Italy (Daniel Jütte) Gian Maria Varanini, Reinhold C. Mueller (Hrsg.): Ebrei nella Terraferma veneta del Quattrocento (Daniel Jütte) Stefanie B. Siegmund: The Medici State and the Ghetto of Florence (Daniel Jütte) Johannes Mordstein: Selbstbewußte Untertänigkeit (Robert Jütte) Werner Heegewaldt, Oliver Sander (Hrsg.): Salomo Sachs (Elvira Grözinger) Philipp Theisohn: Die Urbarkeit der Zeichen. Zionismus und Literatur - eine andere Poetik der Moderne (Joachim Schlör) Jascha Nemtsov: Die Neue Jüdische Schule in der Musik (Susanne Hudak-Laziç) Ines Sonder: Gartenstädte in Eretz Israel. (Robert Jütte) Cilly Kugelmann (Hrsg.): Weihnukka. Geschichten von Weihnachten und Chanukka. (Daniel Jütte) Moshe Zimmermann, Yotam Hotam (Hrsg.): Zweimal Heimat. Die Jeckes zwischen Mitteleuropa und Nahost. (Anat Feinberg) Birgit Schlachter: Schreibweisen der Abwesenheit. (Elvira Grözinger) Jüdische Studien in aller Welt: Juden und Judentum im Iran - Einige zufällige und weniger zufällige Reiseeindrücke (Hans-Michael Haußig) Nachrichten Rückblicke
Wie nicht erinnern?
(2006)
John Birks
(2015)
We describe the career of John Birks as a pioneering scientist who has, over a career spanning five decades, transformed palaeoecology from a largely descriptive to a rigorous quantitative science relevant to contemporary questions in ecology and environmental change. We review his influence on students and colleagues not only at Cambridge and Bergen Universities, his places of primary employment, but also on individuals and research groups in Europe and North America. We also introduce the collection of papers that we have assembled in his honour. The papers are written by his former students and close colleagues and span many of the areas of palaeoecology to which John himself has made major contributions. These include the relationship between ecology and palaeoecology, late-glacial and Holocene palaeoecology, ecological succession, climate change and vegetation history, the role of palaeoecological techniques in reconstructing and understanding the impact of human activity on terrestrial and freshwater ecosystems and numerical analysis of multivariate palaeoecological data.
Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81
(2016)
The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11–646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.
Src1 is a Protein of the Inner Nuclear Membrane Interacting with the Dictyostelium Lamin NE81
(2016)
The nuclear envelope (NE) consists of the outer and inner nuclear membrane (INM), whereby the latter is bound to the nuclear lamina. Src1 is a Dictyostelium homologue of the helix-extension-helix family of proteins, which also includes the human lamin-binding protein MAN1. Both endogenous Src1 and GFP-Src1 are localized to the NE during the entire cell cycle. Immuno-electron microscopy and light microscopy after differential detergent treatment indicated that Src1 resides in the INM. FRAP experiments with GFP-Src1 cells suggested that at least a fraction of the protein could be stably engaged in forming the nuclear lamina together with the Dictyostelium lamin NE81. Both a BioID proximity assay and mis-localization of soluble, truncated mRFP-Src1 at cytosolic clusters consisting of an intentionally mis-localized mutant of GFP-NE81 confirmed an interaction of Src1 and NE81. Expression GFP-Src11–646, a fragment C-terminally truncated after the first transmembrane domain, disrupted interaction of nuclear membranes with the nuclear lamina, as cells formed protrusions of the NE that were dependent on cytoskeletal pulling forces. Protrusions were dependent on intact microtubules but not actin filaments. Our results indicate that Src1 is required for integrity of the NE and highlight Dictyostelium as a promising model for the evolution of nuclear architecture.
A lamin in lower eukaryotes?
(2012)
Lamins are the major components of the nuclear lamina and serve not only as a mechanical support, but are also involved in chromatin organization, epigenetic regulation, transcription and mitotic events. Despite these universal tasks, lamins have so far been found only in metazoans. Yet, recently we have identified Dictyostelium NE81 as the first lamin-like protein in a lower eukaryote. Based on the current knowledge, we draw a model for nuclear envelope organization in Dictyostelium in this Extra View and we review the experimental data that justified this classification. Furthermore we provide unpublished data underscoring the requirement of posttranslational CaaX-box processing for proper protein localization at the nuclear envelope. Sequence comparison of NE81 sequences from four Dictyostelia with bona fide lamins illustrates the evolutional relationship between these proteins. Under certain conditions these usually unicellular social amoebae congregate to form a multicellular body. We propose that the evolution of the lamin-like NE81 went along with the invention of multicellularity.
The highly conserved enzyme arginyl-tRNA-protein transferase (Ate1) mediates arginylation, a posttranslational modification that is only incompletely understood at its molecular level. To investigate whether arginylation affects actin-dependent processes in a simple model organism, Dictyostelium discoideum, we knocked out the gene encoding Ate1 and characterized the phenotype of ate1-null cells. Visualization of actin cytoskeleton dynamics by live-cell microscopy indicated significant changes in comparison to wild-type cells. Ate1-null cells were almost completely lacking focal actin adhesion sites at the substrate-attached surface and were only weakly adhesive. In two-dimensional chemotaxis assays toward folate or cAMP, the motility of ate1-null cells was increased. However, in three-dimensional chemotaxis involving more confined conditions, the motility of ate1-null cells was significantly reduced. Live-cell imaging showed that GFP-tagged Ate1 rapidly relocates to sites of newly formed actin-rich protrusions. By mass spectrometric analysis, we identified four arginylation sites in the most abundant actin isoform of Dictyostelium, in addition to arginylation sites in other actin isoforms and several actin-binding proteins. In vitro polymerization assays with actin purified from ate1-null cells revealed a diminished polymerization capacity in comparison to wild-type actin. Our data indicate that arginylation plays a crucial role in the regulation of cytoskeletal activities.
The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export.The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun 1, as well as with the LEM/HeH-family protein Src1. Sun 1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun 1 usually forms a so-called LINC complex.Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in perm eabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics.
Business process management is an established technique for business organizations to manage and support their processes. Those processes are typically represented by graphical models designed with modeling languages, such as the Business Process Model and Notation (BPMN).
Since process models do not only serve the purpose of documentation but are also a basis for implementation and automation of the processes, they have to satisfy certain correctness requirements. In this regard, the notion of soundness of workflow nets was developed, that can be applied to BPMN process models in order to verify their correctness. Because the original soundness criteria are very restrictive regarding the behavior of the model, different variants of the soundness notion have been developed for situations in which certain violations are not even harmful.
All of those notions do only consider the control-flow structure of a process model, however. This poses a problem, taking into account the fact that with the recent release and the ongoing development of the Decision Model and Notation (DMN) standard, an increasing number of process models are complemented by respective decision models. DMN is a dedicated modeling language for decision logic and separates the concerns of process and decision logic into two different models, process and decision models respectively.
Hence, this thesis is concerned with the development of decisionaware soundness notions, i.e., notions of soundness that build upon the original soundness ideas for process models, but additionally take into account complementary decision models. Similar to the various notions of workflow net soundness, this thesis investigates different notions of decision soundness that can be applied depending on the desired degree of restrictiveness. Since decision tables are a standardized means of DMN to represent decision logic, this thesis also puts special focus on decision tables, discussing how they can be translated into an unambiguous format and how their possible output values can be efficiently determined.
Moreover, a prototypical implementation is described that supports checking a basic version of decision soundness. The decision soundness notions were also empirically evaluated on models from participants of an online course on process and decision modeling as well as from a process management project of a large insurance company. The evaluation demonstrates that violations of decision soundness indeed occur and can be detected with our approach.
Die Toxizität und Kanzerogenität von rein aromatischen polyzyklischen aromatischen Kohlenwasserstoffen (PAK) ist seit Jahrzehnten bekannt und umfassend erforscht. Die alkylierten PAK (alkPAK) besitzen jedoch aufgrund ihrer Alkylgruppe eine weitere Möglichkeit zur Bioaktivierung und müssen daher gesondert betrachtet werden. Die Alkylgruppe wird zunächst hydroxyliert, anschließend zur Säure oxidiert oder direkt konjugiert. Entstehen hierbei instabile benzylische Sulfokonjugate, so können diese DNA-Addukte bilden und zu Mutationen führen. In Hinblick auf die Bioaktivierung von alkPAK galt es daher zu klären welchen Einfluss die Struktur auf die benzylische Hydroxylierung hat und welche humanen Formen der löslichen Sulfotransferasen besonders an der Umsetzung der alkPAK-Derivate beteiligt sind. Die Untersuchung der Albuminbindung von Schwefelsäureestern sowie ihre Aufnahme in Nierenzellen sollten Aufschluss hinsichtlich möglicher Transportvorgänge geben. Für die in-vivo-Situation wurde weiterhin die Modulation des Metabolismus ausgewählter benzylischer Alkohole durch verschiedene Nahrungsmittelbestandteile, Arzneimittel und Fremdstoffe an Ratten untersucht. Als Biomarker wurden benzylische Carbonsäuren im Urin und die entsprechenden Mercaptursäuren in Urin und Fäzes betrachtet. Zunächst wurde anhand von Inkubationen mit Rattenlebermikrosomen festgestellt, dass insbesondere größere Ringsystemen wie etwa alkylierte Benzo[a]pyrene im Gegensatz zu Methylpyrenen in wesentlich geringerem Umfang zum benzylischen Alkohol umgesetzt werden. Dies wurde auch in Untersuchungen mit humanen Lebermikrosomen bestätigt. Untersuchungen an einzelnen humanen Cytochromen P450 zeigten, dass insbesondere die durch PAK induzierbaren Formen hCYP1A1 und 1B1 hohe Umsatzraten aufwiesen. Die hepatisch exprimierten Formen hCYP1A2 und 3A4 waren jedoch auch zur Bildung der benzylischen Alkohole in der Lage. Für die anschließende Sulfonierung der benzylischen Alkohole wurden besonders hohe Aktivitäten mit den humanen Sulfotransferasen hSULT1A1, 1A2, 1C2 und 1E1 festgestellt. Aufgrund der Enzymexpression und der guten Durchblutung, die eine gute Substratversorgung ermöglicht, ist die Leber als Hauptort der benzylischen Hydroxylierung und Sulfonierung anzusehen. Ergebnisse unserer Arbeitsgruppe zeigen jedoch, dass nach 1-Hydroxymethylpyren-Applikation bei Ratten die Niere die höchste Zahl an DNA-Addukten aufweist. Wegen der Fokussierung der Sulfonierung auf die Leber ist die systemische Verteilung der Schwefelsäureester die einzig plausible Erklärung. So wurde im Rahmen dieser Arbeit eine hochaffine Bindungsstelle für 2-Sulfoxymethylpyren an Albumin beschrieben und die Aufnahme von benzylischen Sulfaten durch die humanen organischen Anionentransporter hOAT1, 3 und 4 in Nierenzellen in vitro gezeigt. Für die in-vivo-Situation wurde der Einfluss von Ethanol, 4-Methylpyrazol, Pentachlorphenol, Quercetin und Disulfiram untersucht. Neben der durch die Detoxifizierung mittels Alkoholdehydrogenase und Aldehyddehydrogenase entstandenen benzylischen Carbonsäure kann als Biomarker die entsprechende Mercaptursäure herangezogen werden. Sie ist ein indirekter Nachweis für die reaktiven und toxischen benzylischen Sulfate der alkPAK. Für die beiden im Tierversuch eingesetzten benzylischen Alkohole (1-Hydroxymethylpyren und 1-Hydroxymethyl-8-methylpyren) konnte sie in Urin und Fäzes nachgewiesen werden. Es wurde jedoch ein deutlicher Unterschied in der gebildeten Menge sowie der Verteilung zwischen Urin und Fäzes für die beiden Mercaptursäuren festgestellt. Hierfür sind wahrscheinlich Unterschiede im Transport der benzylischen Schwefelsäureester sowie der Spezifität der an der Mercaptursäurebildung beteiligten Enzyme verantwortlich. In diesem Zusammenhang konnte gezeigt werden, dass der humane organische Anionentransporter hOAT1 1,8-Dimethylpyrenmercaptursäure nicht und der hOAT3 nur mit niedrigen Umsatzraten transportiert. Bei den Modulatoren zeigte die Gabe der kompetitiven Alkoholdehydrogenase-Hemmstoffe Ethanol und 4-Methylpyrazol die Bedeutung der Alkoholdehydrogenasen für die Entgiftung der benzylischen Alkohole: Die Oxidation zur entsprechenden Carbonsäure war reduziert und die Bildung der Mercaptursäure erhöht. Eine Hemmung der Toxifizierung vermittelt durch Sulfotransferase-Inhibitoren konnte nur für Pentachlorphenol beim Metabolismus des 1-Hydroxymethylpyrens beobachtet werden. Gleichzeitig erwies sich Pentachlorphenol als kompetitiver Alkoholdehydrogenase-Inhibitor, da eine signifikant geminderte Carbonsäureausscheidung zu beobachten war. Bei 1-Hydroxymethyl-8-methylpyren traten diese Effekte nicht auf. Die unterschiedlichen bzw. unterschiedlich starken Effekte der Modulatoren beim Metabolismus der verschiedenen benzylischen Alkohole bestätigen die Beobachtungen aus den in-vitro-Untersuchungen, dass unterschiedliche Enzym- und Transporteraffinitäten und –aktivitäten vorliegen.
MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
The endosperm is an ephemeral tissue that nourishes the developing embryo, similar to the placenta in mammals. In most angiosperms, endosperm development starts as a syncytium, in which nuclear divisions are not followed by cytokinesis. The timing of endosperm cellularization largely varies between species, and the event triggering this transition remains unknown. Here we show that increased auxin biosynthesis in the endosperm prevents its cellularization, leading to seed arrest. Auxin-overproducing seeds phenocopy paternal-excess triploid seeds derived from hybridizations of diploid maternal plants with tetraploid fathers. Concurrently, auxin-related genes are strongly overexpressed in triploid seeds, correlating with increased auxin activity. Reducing auxin biosynthesis and signaling reestablishes endosperm cellularization in triploid seeds and restores their viability, highlighting a causal role of increased auxin in preventing endosperm cellularization. We propose that auxin determines the time of endosperm cellularization, and thereby uncovered a central role of auxin in establishing hybridization barriers in plants.
Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities.
Although ring faults are present at many ancient, deeply eroded volcanoes, they have been detected at only very few modern volcanic centers. At the so far little studied Tendurek volcano in eastern Turkey, we generated an ascending and a descending InSAR time series of its surface displacement field for the period from 2003 to 2010. We detected a large (similar to 105km(2)) region that underwent subsidence at the rate of similar to 1cm/yr during this period. Source modeling results show that the observed signal fits best to simulations of a near-horizontal contracting sill located at around 4.5km below the volcano summit. Intriguingly, the residual displacement velocity field contains a steep gradient that systematically follows a system of arcuate fractures visible on the volcano’s midflanks. RapidEye satellite optical images show that this fracture system has deflected Holocene lava flows, thus indicating its presence for at least several millennia. We interpret the arcuate fracture system as the surface expression of an inherited ring fault that has been slowly reactivated during the detected recent subsidence. These results show that volcano ring faults may not only slip rapidly during eruptive or intrusive phases, but also slowly during dormant phases.
Surface displacement at volcanic edifices is related to subsurface processes associated with magma movements, fluid transfers within the volcano edifice and gravity-driven deformation processes. Understanding of associated ground displacements is of importance for assessment of volcanic hazards. For example, volcanic unrest is often preceded by surface uplift, caused by magma intrusion and followed by subsidence, after the withdrawal of magma. Continuous monitoring of the surface displacement at volcanoes therefore might allow the forecasting of upcoming eruptions to some extent. In geophysics, the measured surface displacements allow the parameters of possible deformation sources to be estimated through analytical or numerical modeling. This is one way to improve the understanding of subsurface processes acting at volcanoes. Although the monitoring of volcanoes has significantly improved in the last decades (in terms of technical advancements and number of monitored volcanoes), the forecasting of volcanic eruptions remains puzzling. In this work I contribute towards the understanding of the subsurface processes at volcanoes and thus to the improvement of volcano eruption forecasting. I have investigated the displacement field of Llaima volcano in Chile and of Tendürek volcano in East Turkey by using synthetic aperture radar interferometry (InSAR). Through modeling of the deformation sources with the extracted displacement data, it was possible to gain insights into potential subsurface processes occurring at these two volcanoes that had been barely studied before. The two volcanoes, although of very different origin, composition and geometry, both show a complexity of interacting deformation sources. At Llaima volcano, the InSAR technique was difficult to apply, due to the large decorrelation of the radar signal between the acquisition of images. I developed a model-based unwrapping scheme, which allows the production of reliable displacement maps at the volcano that I used for deformation source modeling. The modeling results show significant differences in pre- and post-eruptive magmatic deformation source parameters. Therefore, I conjecture that two magma chambers exist below Llaima volcano: a post-eruptive deep one and a shallow one possibly due to the pre-eruptive ascent of magma. Similar reservoir depths at Llaima have been confirmed by independent petrologic studies. These reservoirs are interpreted to be temporally coupled. At Tendürek volcano I have found long-term subsidence of the volcanic edifice, which can be described by a large, magmatic, sill-like source that is subject to cooling contraction. The displacement data in conjunction with high-resolution optical images, however, reveal arcuate fractures at the eastern and western flank of the volcano. These are most likely the surface expressions of concentric ring-faults around the volcanic edifice that show low magnitudes of slip over a long time. This might be an alternative mechanism for the development of large caldera structures, which are so far assumed to be generated during large catastrophic collapse events. To investigate the potential subsurface geometry and relation of the two proposed interacting sources at Tendürek, a sill-like magmatic source and ring-faults, I have performed a more sophisticated numerical modeling approach. The optimum source geometries show, that the size of the sill-like source was overestimated in the simple models and that it is difficult to determine the dip angle of the ring-faults with surface displacement data only. However, considering physical and geological criteria a combination of outward-dipping reverse faults in the west and inward-dipping normal faults in the east seem to be the most likely. Consequently, the underground structure at the Tendürek volcano consists of a small, sill-like, contracting, magmatic source below the western summit crater that causes a trapdoor-like faulting along the ring-faults around the volcanic edifice. Therefore, the magmatic source and the ring-faults are also interpreted to be temporally coupled. In addition, a method for data reduction has been improved. The modeling of subsurface deformation sources requires only a relatively small number of well distributed InSAR observations at the earth’s surface. Satellite radar images, however, consist of several millions of these observations. Therefore, the large amount of data needs to be reduced by several orders of magnitude for source modeling, to save computation time and increase model flexibility. I have introduced a model-based subsampling approach in particular for heterogeneously-distributed observations. It allows a fast calculation of the data error variance-covariance matrix, also supports the modeling of time dependent displacement data and is, therefore, an alternative to existing methods.
Veränderung der Carotinoidkonzentration im Serum und in der Milch im Verlauf der Laktation der Frau
(2000)
Moving spiral wave chimeras
(2021)
We consider a two-dimensional array of heterogeneous nonlocally coupled phase oscillators on a flat torus and study the bound states of two counter-rotating spiral chimeras, shortly two-core spiral chimeras, observed in this system. In contrast to other known spiral chimeras with motionless incoherent cores, the two-core spiral chimeras typically show a drift motion. Due to this drift, their incoherent cores become spatially modulated and develop specific fingerprint patterns of varying synchrony levels. In the continuum limit of infinitely many oscillators, the two-core spiral chimeras can be studied using the Ott-Antonsen equation. Numerical analysis of this equation allows us to reveal the stability region of different spiral chimeras, which we group into three main classes-symmetric, asymmetric, and meandering spiral chimeras.
Bioinspired confinement of upconversion nanoparticles for improved performance in aqueous solution
(2020)
The resonance energy transfer (RET) from NaYF4:Yb,Er upconverting nanoparticles (UNCPs) to a dye (5-carboxytetramethylrhodamine (TAMRA)) was investigated by photoluminescence experiments and microscale thermophoresis (MST). The dye was excited via RET from the UCNPs which was excited in the near-infrared (NIR). The change of the dye diffusion speed (free vs coupled) was investigated by MST. RET shows significant changes in the decay times of the dye as well as of the UCNPs. MST reveals significant changes in the diffusion speed. A unique amphiphilic coating polymer (customized mussel protein (CMP) polymer) for UCNP surface coating was used, which mimics blood protein adsorption and mussel food protein adhesion to transfer the UCNP into the aqueous phase and to allow surface functionalization. The CMP provides very good water dispersibility to the UCNPs and minimizes ligand exchange and subsequent UCNP aging reactions because of the interlinkage of the CMP on the UCNP surface. Moreover, CMP provides N-3-functional groups for dick chemistry-based functionalization demonstrated with the dye 5-carboxytetramethylrhodamine (TAMRA). This establishes the principle coupling scheme for suitable biomarkers such as antibodies. The CMP provides very stable aqueous UCNP dispersions that are storable up to 3 years in a fridge at 5 degrees C without dissolution or coagulation. The outstanding properties of CMP in shielding the UCNP from unwanted solvent effects is reflected in the distinct increase of the photoluminescence decay times after UCNP functionalization. The UCNP-to-TAMRA energy transfer is also spectroscopically investigated at low temperatures (4-200 K), revealing that one of the two green Er(III) emission bands contributes the major part to the energy transfer. The TAMRA fluorescence decay time increases by a factor of 9500 from 2.28 ns up to 22 mu s due to radiationless energy transfer from the UCNP after NIR excitation of the latter. This underlines the unique properties of CMP as a versatile capping ligand for distinctly improving the UCNPs' performance in aqueous solutions, for coupling of biomolecules, and for applications for in vitro and in vivo experiments using UCNPs as optical probes in life science applications.
The imagination of clearly separated core-shell structures is already outdated by the fact, that the nanoparticle core-shell structures remain in terms of efficiency behind their respective bulk material due to intermixing between core and shell dopant ions. In order to optimize the photoluminescence of core-shell UCNP the intermixing should be as small as possible and therefore, key parameters of this process need to be identified. In the present work the Ln(III) ion migration in the host lattices NaYF4 and NaGdF4 was monitored. These investigations have been performed by laser spectroscopy with help of lanthanide resonance energy transfer (LRET) between Eu(III) as donor and Pr(III) or Nd(III) as acceptor. The LRET is evaluated based on the Forster theory. The findings corroborate the literature and point out the migration of ions in the host lattices. Based on the introduced LRET model, the acceptor concentration in the surrounding of one donor depends clearly on the design of the applied core-shell-shell nanoparticles. In general, thinner intermediate insulating shells lead to higher acceptor concentration, stronger quenching of the Eu(III) donor and subsequently stronger sensitization of the Pr(III) or the Nd(III) acceptors. The choice of the host lattice as well as of the synthesis temperature are parameters to be considered for the intermixing process.