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Galaxies evolve on cosmological timescales and to study this evolution we can either study the stellar populations, tracing the star formation and chemical enrichment, or the dynamics, tracing interactions and mergers of galaxies as well as accretion. In the last decades this field has become one of the most active research areas in modern astrophysics and especially the use of integral field spectrographs furthered our understanding. This work is based on data of NGC 5102 obtained with the panoramic integral field spectrograph MUSE. The data are analysed with two separate and complementary approaches: In the first part, standard methods are used to measure the kinematics and than model the gravitational potential using these exceptionally high-quality data. In the second part I develop the new method of surface brightness fluctuation spectroscopy and quantitatively explore its potential to investigate the bright evolved stellar population.
Measuring the kinematics of NGC 5102 I discover that this low-luminosity S0 galaxy hosts two counter rotating discs. The more central stellar component co-rotates with the large amount of HI gas. Investigating the populations I find strong central age and metallicity gradients with a younger and more metal rich central population. The spectral resolution of MUSE does not allow to connect these population gradients with the two counter rotating discs.
The kinematic measurements are modelled with Jeans anisotropic models to infer the gravitational potential of NGC 5102. Under the self-consistent mass-follows-light assumption none of the Jeans models is able to reproduce the observed kinematics. To my knowledge this is the strongest evidence evidence for a dark matter dominated system obtained with this approach so far. Including a Navarro, Frenk & White dark matter halo immediately solves the discrepancies. A very robust result is the logarithmic slope of the total matter density. For this low-mass galaxy I find a value of -1.75 +- 0.04, shallower than an isothermal halo and even shallower than published values for more massive galaxies. This confirms a tentative relation between total mass slope and stellar mass of galaxies.
The Surface Brightness Fluctuation (SBF) method is a well established distance measure, but due to its sensitive to bright stars also used to study evolved stars in unresolved stellar populations. The wide-field spectrograph MUSE offers the possibility to apply this technique for the first time to spectroscopic data. In this thesis I develop the spectroscopic SBF technique and measure the first SBF spectrum of any galaxy. I discuss the challenges for measuring SBF spectra that rise due to the complexity of integral field spectrographs compared to imaging instruments.
Since decades, stellar population models indicate that SBFs in intermediate-to-old stellar systems are dominated by red giant branch and asymptotic giant branch stars. Especially the later carry significant model uncertainties, making these stars a scientifically interesting target. Comparing the NGC 5102 SBF spectrum with stellar spectra I show for the first time that M-type giants cause the fluctuations. Stellar evolution models suggest that also carbon rich thermally pulsating asymptotic giant branch stars should leave a detectable signal in the SBF spectrum. I cannot detect a significant contribution from these stars in the NGC 5102 SBF spectrum.
I have written a stellar population synthesis tool that predicts for the first time SBF spectra. I compute two sets of population models: based on observed and on theoretical stellar spectra. In comparing the two models I find that the models based on observed spectra predict weaker molecular features. The comparison with the NGC 5102 spectrum reveals that these models are in better agreement with the data.
Hintergrund
Für Patienten mit hochgradiger Aortenklappenstenose, die aufgrund ihres Alters oder ihrer Multimorbidität ein hohes Operationsrisiko tragen, konnte mit der kathetergestützten Aortenklappenkorrektur (transcatheter aortic valve implantation, TAVI) eine vielversprechende Alternative zum herzchirurgischen Eingriff etabliert werden. Explizite Daten zur multidisziplinären kardiologischen Rehabilitation nach TAVI liegen bislang nicht vor. Ziel vorliegender Arbeit war, den Effekt der kardiologischen Rehabilitation auf die körperliche Leistungsfähigkeit, den emotionalen Status, die Lebensqualität und die Gebrechlichkeit bei Patienten nach TAVI zu untersuchen sowie Prädiktoren für die Veränderung der körperlichen Leistungsfähigkeit und der Lebensqualität zu identifizieren.
Methodik
Zwischen 10/2013 und 07/2015 wurden 136 Patienten (80,6 ± 5,0 Jahre, 47,8 % Männer) in Anschlussheilbehandlung nach TAVI in drei kardiologischen Rehabilitationskliniken eingeschlossen. Zur Beurteilung des Effekts der kardiologischen Rehabilitation wurden jeweils zu Beginn und Ende der Rehabilitation der Frailty (Gebrechlichkeits)-Index (Score bestehend aus Barthel-Index, Instrumental Activities of Daily Living, Mini Mental State Exam, Mini Nutritional Assessment, Timed Up and Go und subjektiver Mobilitätsverschlechterung), die Lebensqualität im Short-Form 12 (SF-12) sowie die funktionale körperliche Leistungsfähigkeit im 6-Minuten Gehtest (6-minute walk test, 6MWT) und die maximale körperliche Leistungsfähigkeit in der Belastungs-Ergometrie erhoben. Zusätzlich wurden soziodemographische Daten (z. B. Alter und Geschlecht), Komorbiditäten (z. B. chronisch obstruktive Lungenerkrankung, koronare Herzkrankheit und Karzinom), kardiovaskuläre Risikofaktoren und die NYHA-Klasse dokumentiert. Prädiktoren für die Veränderung der körperlichen Leistungsfähigkeit und Lebensqualität wurden mit Kovarianzanalysen angepasst.
Ergebnisse
Die maximale Gehstrecke im 6MWT konnte um 56,3 ± 65,3 m (p < 0,001) und die maximale körperliche Leistungsfähigkeit in der Belastungs-Ergometrie um 8,0 ± 14,9 Watt (p < 0001) gesteigert werden. Weiterhin konnte eine Verbesserung im SF-12 sowohl in der körperlichen Summenskala um 2,5 ± 8,7 Punkte (p = 0,001) als auch in der psychischen Summenskala um 3,4 ± 10,2 Punkte (p = 0,003) erreicht werden. In der multivariaten Analyse waren ein höheres Alter und eine höhere Bildung signifikant mit einer geringeren Zunahme im 6MWT assoziiert, währenddessen eine bessere kognitive Leistungsfähigkeit und Adipositas einen positiven prädiktiven Wert aufwiesen. Eine höhere Selbstständigkeit und ein besserer Ernährungsstatus beeinflussten die Veränderung in der körperlichen Summenskala des SF-12 positiv, währenddessen eine bessere kognitive Leistungsfähigkeit einen Prädiktor für eine geringere Veränderung darstellte. Des Weiteren hatten die jeweiligen Ausgangswerte der körperlichen und psychischen Summenskala im SF-12 einen inversen Einfluss auf die Veränderungen in der gleichen Skala.
Schlussfolgerung
Eine multidisziplinäre kardiologische Rehabilitation kann sowohl die körperliche Leistungs-fähigkeit und Lebensqualität verbessern als auch die Gebrechlichkeit von Patienten nach kathetergestützter Aortenklappenkorrektur verringern. Daraus resultierend gilt es, spezifische Assessments für die kardiologische Rehabilitation zu entwickeln. Weiterhin ist es notwendig, individualisierte Therapieprogramme mit besonderem Augenmerk auf kognitive Funktionen und Ernährung zu initiieren, um die Selbstständigkeit hochbetagter Patienten zu erhalten bzw. wiederherzustellen und um die Pflegebedürftigkeit der Patienten hinauszuzögern.
The ionosphere, which is strongly influenced by the Sun, is known to be also affected by meteorological processes. These processes, despite having their origin in the troposphere and stratosphere, interact with the upper atmosphere. Such an interaction between atmospheric layers is known as vertical coupling. During geomagnetically quiet times, when near-Earth space is not under the influence of solar storms, these processes become important drivers for ionospheric variability. Studying the link between these processes in the lower atmosphere and the ionospheric variability is important for our understanding of fundamental mechanisms in ionospheric and meteorological research.
A prominent example of vertical coupling between the stratosphere and the ionosphere are the so-called stratospheric sudden warming (SSW) events that occur usually during northern winters and result in an increase in the polar stratospheric temperature and a reversal of the circumpolar winds. While the phenomenon of SSW is confined to the northern polar stratosphere, its influence on the ionosphere can be observed even at equatorial latitudes. During SSW events, the connection between the polar stratosphere and the equatorial ionosphere is believed to be through the modulation of global atmospheric tides. These tides are fundamental for the ionospheric E-region wind dynamo that generates electric fields and currents in the ionosphere. Observations of ionospheric currents indicate a large enhancement of the semidiurnal lunar tide in response to SSW events. Thus, the semidiurnal lunar tide becomes an important driver of ionospheric variability during SSW events.
In this thesis, the ionospheric effect of SSW events is investigated in the equatorial region, where a narrow but an intense E-region current known as the equatorial electrojet (EEJ) flows above the dip equator during the daytime. The day-to-day variability of the EEJ can be determined from magnetic field records at geomagnetic observatories close to the dip equator. Such magnetic data are available for several decades and allows to investigate the impact of SSW events on the EEJ and, even more importantly, helps in understanding the effects of SSW events on the equatorial ionosphere. An excellent long-term record of the geomagnetic field at the equator from 1922 onwards is available for the observatory Huancayo in Peru and is extensively utilized in this study.
The central subject of this thesis is the investigation of lunar tides in the EEJ during SSW events by analyzing long time series. This is done by estimating the lunar tidal amplitude in the EEJ from the magnetic records at Huancayo and by comparing them to measurements of the polar stratospheric wind and temperature, which led to the identification of the known SSW events from 1952 onwards. One goal of this thesis is to identify SSW events that predate 1952. To this end, superposed epoch analysis (SEA) is employed to establish a relationship between the lunar tidal power and the wind and temperature conditions in the lower atmosphere. A threshold value for the lunar tidal power is identified that is discriminative for the known SSW events. This threshold is then used to identify lunar tidal enhancements, which are indicative for any historic SSW events prior to 1952. It can be shown, that the number of lunar tidal enhancements and thus the occurrence frequency of historic SSW events between 1926 and 1952 is similar to the occurrence frequency of the known SSW events from 1952 onwards.
Next to the classic SSW definition, the concept of polar vortex weakening (PVW) is utilized in this thesis. PVW is defined for higher latitudes and altitudes (≈ 40km) than the classical SSW definition (≈ 32km). The correlation between the timing and magnitude of lunar tidal enhancements in the EEJ and the timing and magnitude of PVW is found to be better than for the classic SSW definition. This suggests that the lunar tidal enhancements in the EEJ are closely linked to the state of the middle atmosphere.
Geomagnetic observatories located in different longitudes at the dip equator allow investigating the longitudinally dependent variability of the EEJ during SSW events. For this purpose, the lunar tidal enhancements in the EEJ are determined for the Peruvian and Indian sectors during the major SSW events of the years 2006 and 2009. It is found that the lunar tidal amplitude shows similar enhancements in the Peruvian sector during both SSW events, while the enhancements are notably different for the two events in the Indian sector.
In summary, this thesis shows that lunar tidal enhancements in the EEJ are indeed correlated to the occurrence of SSW events and they should be considered a prominent driver of low latitude ionospheric variability. Secondly, lunar tidal enhancements are found to be longitudinally variable. This suggests that regional effects, such as ionospheric conductivity and the geometry and strength of the geomagnetic field, also play an important role and have to be considered when investigating the mechanisms behind vertical coupling.
In dieser Arbeit werden drei Themen im Zusammenhang mit den spektroskopischen Eigenschaften von Cumarin- (Cou) und DBD-Farbstoffen ([1,3]Dioxolo[4,5-f][1,3]benzodioxol) behandelt. Der erste Teil zeigt die grundlegende spektroskopische Charakterisierung von 7-Aminocumarinen und ihre potentielle Anwendung als Fluoreszenzsonde für Fluoreszenzimmunassays. Im zweiten Teil werden mit die photophysikalischen Eigenschaften der Cumarine genutzt um Cou- und DBD-funktionalisierte Oligo-Spiro-Ketal-Stäbe (OSTK) und ihre Eigenschaften als Membransonden zu untersuchen. Der letzte Teil beschäftigt sich mit der Synthese und der Charakterisierung von Cou- und DBD-funktionalisierten Polyprolinen als Referenzsysteme für schwefelfunktionalisierte OSTK-Stäbe und ihrer Kopplung an Goldnanopartikel.
Immunochemische Analysemethoden sind in der klinischen Diagnostik sehr erfolgreich und werden heute auch für die Nahrungsmittelkontrolle und Überwachung von Umweltfragen mit einbezogen. Dadurch sind sie von großem Interesse für weitere Forschungen. Unter den verschiedenen Immunassays zeichnen sich lumineszenzbasierte Formate durch ihre herausragende Sensitivität aus, die dieses Format für zukünftige Anwendungen besonders attraktiv macht. Die Notwendigkeit von Multiparameterdetektionsmöglichkeiten erfordert einen Werkzeugkasten mit Farbstoffen, um die biochemische Reaktion in ein optisch detektierbares Signal umzuwandeln. Hier wird bei einem Multiparameteransatz jeder Analyt durch einen anderen Farbstoff mit einer einzigartigen Emissionsfarbe, die den blauen bis roten Spektralbereich abdecken, oder eine einzigartige Abklingzeit detektiert. Im Falle eines kompetitiven Immunassayformats wäre für jeden der verschiedenen Farbstoffe ein einzelner Antikörper erforderlich. In der vorliegenden Arbeit wird ein leicht modifizierter Ansatz unter Verwendung einer Cumarineinheit, gegen die hochspezifische monoklonale Antikörper (mAb) erzeugt wurden, als grundlegendes Antigen präsentiert. Durch eine Modifikation der Stammcumarineinheit an einer Position des Moleküls, die für die Erkennung durch den Antikörper nicht relevant ist, kann auf den vollen Spektralbereich von blau bis tiefrot zugegriffen werden. In dieser Arbeit wird die photophysikalische Charakterisierung der verschiedenen Cumarinderivate und ihrer entsprechenden Immunkomplexe mit zwei verschiedenen, aber dennoch hochspezifischen, Antikörpern präsentiert. Die Cumarinfarbstoffe und ihre Immunkomplexe wurden durch stationäre und zeitaufgelöste Absorptions- sowie Fluoreszenzemissionsspektroskopie charakterisiert. Darüber hinaus wurden Fluoreszenzdepolarisationsmessungen durchgeführt, um die Daten zu vervollständigen, die die verschiedenen Bindungsmodi der beiden Antikörper betonten. Im Gegensatz zu häufig eingesetzten Nachweissystemen wurde eine massive Fluoreszenzverstärkung bei der Bildung des Antikörper-Farbstoffkomplexes bis zu einem Faktor von 50 gefunden. Wegen der leichten Emissionsfarbenänderung durch das Anpassen der Cumarinsubstitution in der für die Antigenbindung nicht relevanten Position des Elternmoleküls, ist eine Farbstoff-Toolbox vorhanden, die bei der Konstruktion von kompetitiven Multiparameterfluoreszenzverstärkungsimmunassays verwendet werden kann.
Oligo-Spiro-Thio-Ketal-Stäbe werden aufgrund ihres hydrophoben Rückgrats leicht in Doppellipidschichten eingebaut und deshalb als optische Membransonde verwendet. Wegen ihres geringen Durchmessers wird nur eine minimale Störung der Doppellipidschicht verursacht. Durch die Markierung mit Fluoreszenzfarbstoffen sind neuartige Förster-Resonanz-Energietransfersonden mit hoch definierten relativen Orientierungen der Übergangsdipolmomente der Donor- und Akzeptorfarbstoffe zugänglich und macht die Klasse der OSTK-Sonden zu einem leistungsstarken, flexiblen Werkzeugkasten für optische Biosensoranwendungen. Mit Hilfe von stationären und zeitaufgelösten Fluoreszenzexperimenten wurde der Einbau von Cumarin- und DBD markierten OSTK-Stäben in großen unilamellaren Vesikeln untersucht und die Ergebnisse durch Fluoreszenzdepolarisationsmessungen untermauert.
Der letzte Teil dieser Arbeit beschäftigt sich mit der Synthese und Charakterisierung von Cou- und DBD-funktionalisierten Polyprolinen und ihrer Kopplung an Goldnanopartikel. Die farbstoffmarkierten Polyproline konnten erfolgreich hergestellt werden. Es zeigten sich deutlich Einflüsse auf die spektroskopischen Eigenschaften der Farbstoffe durch die Bindung an die Polyprolinhelix. Die Kopplung an die 5 nm großen AuNP konnte erfolgreich durchgeführt werden. Die Erfahrungen, die durch die Kopplung der Polyproline an die AuNP, gewonnen wurde, ist die Basis für eine Einzelmolekül-AFM-FRET-Nanoskopie mit OSTK-Stäben.
Personal Big Data
(2017)
Many users of cloud-based services are concerned about questions of data privacy. At the same time, they want to benefit from smart data-driven services, which require insight into a person’s individual behaviour. The modus operandi of user modelling is that data is sent to a remote server where the model is constructed and merged with other users’ data. This thesis proposes selective cloud computing, an alternative approach, in which the user model is constructed on the client-side and only an abstracted generalised version of the model is shared with the remote services.
In order to demonstrate the applicability of this approach, the thesis builds an exemplary client-side user modelling technique. As this thesis is carried out in the area of Geoinformatics and spatio-temporal data is particularly sensitive, the application domain for this experiment is the analysis and prediction of a user’s spatio-temporal behaviour.
The user modelling technique is grounded in an innovative conceptual model, which builds upon spatial network theory combined with time-geography. The spatio-temporal constraints of time-geography are applied to the network structure in order to create individual spatio-temporal action spaces. This concept is translated into a novel algorithmic user modelling approach which is solely driven by the user’s own spatio-temporal trajectory data that is generated by the user’s smartphone.
While modern smartphones offer a rich variety of sensory data, this thesis only makes use of spatio-temporal trajectory data, enriched by activity classification, as the input and foundation for the algorithmic model. The algorithmic model consists of three basal components: locations (vertices), trips (edges), and clusters (neighbourhoods).
After preprocessing the incoming trajectory data in order to identify locations, user feedback is used to train an artificial neural network to learn temporal patterns for certain location types (e.g. work, home, bus stop, etc.). This Artificial Neural Network (ANN) is used to automatically detect future location types by their spatio-temporal patterns. The same is done in order to predict the duration of stay at a certain location. Experiments revealed that neural nets were the most successful statistical and machine learning tool to detect those patterns. The location type identification algorithm reached an accuracy of 87.69%, the duration prediction on binned data was less successful and deviated by an average of 0.69 bins. A challenge for the location type classification, as well as for the subsequent components, was the imbalance of trips and connections as well as the low accuracy of the trajectory data. The imbalance is grounded in the fact that most users exhibit strong habitual patterns (e.g. home > work), while other patterns are rather rare by comparison. The accuracy problem derives from the energy-saving location sampling mode, which creates less accurate results.
Those locations are then used to build a network that represents the user’s spatio-temporal behaviour. An initial untrained ANN to predict movement on the network only reached 46% average accuracy. Only lowering the number of included edges, focusing on more common trips, increased the performance. In order to further improve the algorithm, the spatial trajectories were introduced into the predictions. To overcome the accuracy problem, trips between locations were clustered into so-called spatial corridors, which were intersected with the user’s current trajectory. The resulting intersected trips were ranked through a k-nearest-neighbour algorithm. This increased the performance to 56%. In a final step, a combination of a network and spatial clustering algorithm was built in order to create clusters, therein reducing the variety of possible trips. By only predicting the destination cluster instead of the exact location, it is possible to increase the performance to 75% including all classes.
A final set of components shows in two exemplary ways how to deduce additional inferences from the underlying spatio-temporal data. The first example presents a novel concept for predicting the ‘potential memorisation index’ for a certain location. The index is based on a cognitive model which derives the index from the user’s activity data in that area. The second example embeds each location in its urban fabric and thereby enriches its cluster’s metadata by further describing the temporal-semantic activity in an area (e.g. going to restaurants at noon).
The success of the client-side classification and prediction approach, despite the challenges of inaccurate and imbalanced data, supports the claimed benefits of the client-side modelling concept. Since modern data-driven services at some point do need to receive user data, the thesis’ computational model concludes with a concept for applying generalisation to semantic, temporal, and spatial data before sharing it with the remote service in order to comply with the overall goal to improve data privacy. In this context, the potentials of ensemble training (in regards to ANNs) are discussed in order to highlight the potential of only sharing the trained ANN instead of the raw input data.
While the results of our evaluation support the assets of the proposed framework, there are two important downsides of our approach compared to server-side modelling. First, both of these server-side advantages are rooted in the server’s access to multiple users’ data. This allows a remote service to predict spatio-in the user-specific data, which represents the second downside. While minor classes will likely be minor classes in a bigger dataset as well, for each class, there will still be more variety than in the user-specific dataset. The author emphasises that the approach presented in this work holds the potential to change the privacy paradigm in modern data-driven services. Finding combinations of client- and server-side modelling could prove a promising new path for data-driven innovation.
Beyond the technological perspective, throughout the thesis the author also offers a critical view on the data- and technology-driven development of this work. By introducing the client-side modelling with user-specific artificial neural networks, users generate their own algorithm. Those user-specific algorithms are influenced less by generalised biases or developers’ prejudices. Therefore, the user develops a more diverse and individual perspective through his or her user model. This concept picks up the idea of critical cartography, which questions the status quo of how space is perceived and represented.
In der vorliegenden Arbeit wurden verschiedene Polymere hergestellt, die bestimmte funktionelle Gruppen beinhalten. Diese Gruppen werden zum Teil durch Alkylketten geschützt, zum Teil liegen sie ungeschützt im Polymer vor. Mit diesen Polymeren wurden Untersuchungen mit knochenähnlichen Materialien sogenanntem Calciumphosphat durchgeführt. Es wurde der Einfluss der verschiedenen Polymere auf die Bildung dieser knochenähnlichen Substanzen untersucht und auch der Einfluss auf die Stabilität und das Auflösungsverhalten der Calciumphosphate. Dabei sollte ein besonderes Augenmerk auf die funktionellen Gruppen, sogenannte Phosphonsäuren und deren Ester, die die Phosphonsäuren schützen, gesetzt werden. Es stellte sich heraus, dass bei der Bildung der knochenähnlichen Materialien die Polymere mit Estergruppen eine leichte Förderung der Calciumphosphat-Bildung verursachen, während die ungeschützten Polymere die Bildung des „Knochenmaterials“ sehr stark verzögern. Dieser Effekt verstärkt sich noch, wenn eine weitere bestimmte Komponente zum Polymer hinzukommt und somit ein Copolymer gebildet wird. Diese Copolymere beschleunigen bzw. verlangsamen die Calciumphosphatbildung noch stärker. Werden Polymere mit einem anderen Polymergerüst aber den gleichen Phosphonsäuresetern in den Seitenketten verwendet, ändert sich der Einfluss der Calciumphosphat-Bildung wenig. Verglichen mit Polymeren ohne solche Phosphonsäuregruppen wird erkennbar, dass es weniger die Phosphonsäuregruppe ist, die die Mineralisation beeinflusst, sondern es eher eine Folge der Säure im Polymer ist.
Wird die Stabilisierung und Auflösung der Knochenähnlichen Substanzen betrachtet, fällt auf, dass auch hier wieder die Säuren den größten Effekt ausüben. Die Phosphonsäuregruppen scheinen dabei jedoch tatsächlich einen besonderen Effekt auszuüben, da bei diesen die Stabilisierung und auch das Auflösungsvermögen von Calciumphospaht von allen untersuchten Polymeren am größten sind.
In der Arbeit konnte außerdem gezeigt werden, dass die Polymere und Copolymere mit Phosphonsäuregruppen einen leicht positiven Effekt auf die Zahngesundheit zeigen. Die Zahl von Bakterien auf der Zahnoberfläche konnte reduziert werden und bei der Untersuchung der Zahnauflösung wurde eine glattere Zahnoberfläche erhalten, jedoch wurde auch mit den untersuchten Polymeren der Zahn im Inneren angegriffen. Weitere Untersuchungen können hier noch genaueren Aufschluss geben. Außerdem sollten auch die Polymere mit dem unterschiedlichen Polymergerüst und Phosphonsäureestergruppen untersucht werden.
Letztere Polymere wurden verwendet, um festere “gelartige“ Polymernetzwerke herzustellen und deren Einfluss auf die Calciumphosphatmineralisation zu untersuchen. Es stellte sich heraus, dass ohne das Einbetten einiger Calciumphosphatteilchen keine Bildung von Calciumphospaht an den Materialien ausgelöst wurde, wurden die sogenannten Hydrogele jedoch mit Calciumphosphatpartikeln geimpft, konnte deutliches weiteres Calciumphosphatwachstum beobachtet werden. Das Material lässt sich auch in verschiedene Formen bringen. Somit könnte das System nach weiteren Untersuchungen zur Verträglichkeit mit Zellen oder Geweben ein mögliches Material für Implantate darstellen, mit denen gezielt Knochenwachstum eingeleitet werden könnte.
Prosody is a rich source of information that heavily supports spoken language comprehension. In particular, prosodic phrase boundaries divide the continuous speech stream into chunks reflecting the semantic and syntactic structure of an utterance. This chunking or prosodic phrasing plays a critical role in both spoken language processing and language acquisition. Aiming at a better understanding of the underlying processing mechanisms and their acquisition, the present work investigates factors that influence prosodic phrase boundary perception in adults and infants. Using the event-related potential (ERP) technique, three experimental studies examined the role of prosodic context (i.e., phrase length) in German phrase boundary perception and of the main prosodic boundary cues, namely pitch change, final lengthening, and pause. With regard to the boundary cues, the dissertation focused on the questions which cues or cue combination are essential for the perception of a prosodic boundary and on whether and how this cue weighting develops during infancy.
Using ERPs is advantageous because the technique captures the immediate impact of (linguistic) information during on-line processing. Moreover, as it can be applied independently of specific task demands or an overt response performance, it can be used with both infants and adults. ERPs are particularly suitable to study the time course and underlying mechanisms of boundary perception, because a specific ERP component, the Closure Positive Shift (CPS) is well established as neuro-physiological indicator of prosodic boundary perception in adults.
The results of the three experimental studies first underpin that the prosodic context plays an immediate role in the processing of prosodic boundary information. Moreover, the second study reveals that adult listeners perceive a prosodic boundary also on the basis of a sub-set of the boundary cues available in the speech signal. Both ERP and simultaneously collected behavioral data (i.e., prosodic judgements) suggest that the combination of pitch change and final lengthening triggers boundary perception; however, when presented as single cues, neither pitch change nor final lengthening were sufficient. Finally, testing six- and eight-month-old infants shows that the early sensitivity for prosodic information is reflected in a brain response resembling the adult CPS. For both age groups, brain responses to prosodic boundaries cued by pitch change and final lengthening revealed a positivity that can be interpreted as a CPS-like infant ERP component. In contrast, but comparable to the adults’ response pattern, pitch change as a single cue does not provoke an infant CPS. These results show that infant phrase boundary perception is not exclusively based on pause detection and hint at an early ability to exploit subtle, relational prosodic cues in speech perception.
Throughout all different socio-historical tensions undergone by the Latin American modernit(ies), the literary-historical production as well as the reflection on the topic - regional, national, supranational and/or continental – have been part of the critical and intellectual itinerary of very significant political and cultural projects, whose particular development allows the analysis of the socio-discursive dynamics fulfilled by the literary historiography in the search of a historical conscience and representation of the esthetic-literary processes.
In present literary and cultural Central American literary studies, the academic thought on the development of the literary historiography has given place to some works whose main objects of study involve a significant corpus of national literature histories published mainly in the 20th century, between the forties and the eighties. Although these studies differ greatly from the vast academic production undertaken by the literary critics in the last two decades, the field of research of the literary historiography in Central America has made a theoretical-methodological effort, as of the eighties and until now, to analyze the local literary-historical productions.
However, this effort was carried out more systematically in the last five years of the 20th century, within the Central American democratic transition and post-war context, when a national, supra national and transnational model of literary history was boosted. This gave place to the creation and launching of the project Hacia una Historia de las Literaturas Centroamericanas (HILCAS) at the beginning of the new millennium.
Given the ideological relevance which the literary historiography has played in the process of the historical formation of the Hispano-American States, and whose philological tradition has also had an impact in the various Central American nation states, the emergence of this historiographic project marks an important rupture in relation with the national paradigms, and it is also manifested in a movement of transition and tension with regard to the new cultural, comparative and transareal dynamics, which seek to understand the geographical, transnational, medial and transdisciplinary movements within which the esthetic narrative processes and the idea and formation of a critical Central American subject gain shape.
Taking this aspect into account, our study puts forward as its main hypothesis that the historiographic thought developed as a consequence of the project Hacia una Historia de las Literaturas Centroamericanas (HILCAS) constitutes a socio-discursive practice, which reflects the formation of a historic-literary conscience and of a critical intellectual subject, an emergence that takes place between the mid-nineties and the first decade of the 21st century.
In this respect, and taking as a basis the general purpose of this investigation indicated before, the main justification for our object of study consists of making the Central American historiographic reflection visible as a part of the epistemological and cultural changes shown by the Latin American historiographic thought, and from which a new way of conceptualization of the space, the coexistence and the historic conscience emerge with regard to the esthetic-literary practices and processes.
Based on the field and hypothesis stated before, the general purpose of this research is framed by the socio-discursive dimension fulfilled by the Latin American literary historiography, and it aims to analyze the Central American historical-literary thought developed between the second half of the nineties and the beginning of the first decade of the 21st century.
Der konsularische Schutz
(2017)
Anlässlich der Zunahme von Entführungen deutscher Staatsangehöriger im Ausland und des im Jahr 2009 ergangenen Urteils des Bundesverwaltungsgerichts zu diesem Thema legt die vorliegende Arbeit eine detaillierte und umfassende Analyse der Rechtsgrundlagen für die Gewährung konsularischen Schutzes durch die Auslandsvertretungen der Bundesrepublik Deutschland vor.
Das erste Kapitel beinhaltet eine detaillierte Darstellung der sich aus dem Völker-, Europa- und Verfassungsrecht sowie aus dem Konsulargesetz ergebenen staatlichen Handlungspflichten sowie möglicher damit einhergehender Individualansprüche auf die Ausübung konsularischen Schutzes im Einzelfall.
Im zweiten Kapitel werden die Voraussetzungen der Gewährung konsularischen Schutzes nach dem Konsulargesetz dargestellt. Den Schwerpunkt bildet hierbei die Bestimmung des Anwendungsbereiches des § 5 Abs. 1 Satz 1 Konsulargesetz unter Berücksichtigung des Urteils des Bundesverwaltungsgerichtes vom 28.05.2009, welches nach Auffassung der Verfasserin den Anwendungsbereich dieser Norm verkennt. Bei § 5 Abs. 1 Satz 1 Konsulargesetz handelt es sich um eine besondere sozialhilferechtliche Norm außerhalb der SGB XII, welche die konsularische Hilfe allein in wirtschaftlichen Notlagen regelt.
Das dritte Kapitel analysiert die bestehenden Regelungen über die Erstattung der im Rahmen der Gewährung konsularischen Schutzes entstandenen Kosten und erklärt deren Systematik. Ferner erfolgt ein Ausblick auf die künftigen Regelungen der Kostenerstattung nach dem Bundesgebührengesetz sowie der damit einhergehenden Rechtsverordnung.
Zum Abschluss werden die Ergebnisse anhand eines historischen Falles zusammengefasst sowie ein Gesetzesvorschlag vorgestellt, welcher die gefundenen Unklarheiten und Unstimmigkeiten im Konsulargesetz beheben kann.
Hintergrund: Etablierte Protein- und Nukleinsäure-basierte Methoden für den spezifischen Pathogennachweis sind nur unter standardisierten Laborbedingungen von geschultem Personal durchführbar und daher mit einem hohen Zeit- und Kostenaufwand verbunden. In der Nukleinsäure-basierten Diagnostik kann durch die Einführung der isothermalen Amplifikation eine schnelle und kostengünstige Alternative zur Polymerase-Kettenreaktion (PCR) verwendet werden. Die Loop-mediated isothermal amplification (LAMP) bietet aufgrund der hohen Amplifikationseffizienz vielfältige Detektionsmöglichkeiten, die sowohl für Schnelltest- als auch für Monitoring-Anwendungen geeignet sind.
Ein wesentliches Ziel dieser Arbeit war die Verbesserung der Anwendbarkeit der LAMP und die Entwicklung einer neuen Methode für den einfachen, schnellen und günstigen Nachweis von Pathogenen mittels alternativer DNA- oder Pyrophosphat-abhängiger Detektionsverfahren. Hier wurden zunächst direkte und indirekte Detektionsmethoden untersucht und darauf aufbauend ein Verfahren entwickelt, mit dem neue Metallionen-abhängige Fluoreszenzfarbstoffe für die selektive Detektion von Pyrophosphat in der LAMP und anderen enzymatischen Reaktionen identifiziert werden können. Als Alternative für die DNA-basierte Detektion in der digitalen LAMP sollten die zuvor etablierten Farbstoffe für den Pyrophosphatnachweis in einer Emulsion getestet werden. Abschließend wurde ein neuer Reaktionsmechanismus für die effiziente Generierung hochmolekularer DNA unter isothermalen Bedingungen als Alternative zur LAMP entwickelt.
Ergebnisse: Für den Nachweis RNA- und DNA-basierter Phythopathogene konnte die Echtzeit- und Endpunktdetektion mit verschiedenen Farbstoffen in einem geschlossenen System etabliert werden. Hier wurde Berberin als DNA-interkalierender Fluoreszenzfarbstoff mit vergleichbarer Sensitivität zu SYBR Green und EvaGreen erfolgreich in der LAMP mit Echtzeitdetektion eingesetzt. Ein Vorteil von Berberin gegenüber den anderen Farbstoffen ist die Toleranz der DNA-Polymerase auch bei hohen Farbstoffkonzentrationen. Berberin kann daher auch in der geschlossenen LAMP-Reaktion ohne zusätzliche Anpassung der Reaktionsbedingungen für die Endpunktdetektion verwendet werden. Darüber hinaus konnte Hydroxynaphtholblau (HNB), das für den kolorimetrischen Endpunktnachweis bekannt ist, erstmals auch für die fluorimetrische Detektion der LAMP in Echtzeit eingesetzt werden. Zusätzlich konnten in der Arbeit weitere Metallionen-abhängige Farbstoffe zur indirekten Detektion der LAMP über das Pyrophosphat identifiziert werden. Dafür wurde eine iterative Methode entwickelt, mit der potenzielle Farbstoffe hinsichtlich ihrer Enzymkompatibilität und ihrer spektralen Eigenschaften bei An- oder Abwesenheit von Manganionen selektiert werden können. Mithilfe eines kombinatorischen Screenings im Mikrotiterplattenformat konnte die komplexe Konzentrationsabhängigkeit zwischen den einzelnen Komponenten für einen fluorimetrischen Verdrängungsnachweis untersucht werden. Durch die Visualisierung des Signal-Rausch-Verhältnis’ als Intensitätsmatrix (heatmap) konnten zunächst Alizarinrot S und Tetrazyklin unter simulierten Reaktionsbedingungen selektiert werden. In der anschließenden enzymatischen LAMP-Reaktion konnte insbesondere Alizarinrot S als günstiger, nicht-toxischer und robuster Fluoreszenzfarbstoff identifiziert werden und zeigte eine Pyrophosphat-abhängige Zunahme der Fluoreszenzintensität. Die zuvor etablierten Farbstoffe (HNB, Calcein und Alizarinrot S) konnten anschließend erfolgreich für die indirekte, fluorimetrische Detektion von Pyrophosphat in einer LAMP-optimierten Emulsion eingesetzt werden. Die Stabilität und Homogenität der generierten Emulsion wurde durch den Zusatz des Emulgators Poloxamer 188 verbessert. Durch die fluoreszenzmikroskopische Analyse der Emulsion war eine eindeutige Diskriminierung der positiven und negativen Tröpfchen vor allem bei Einsatz von Calcein und Alizarinrot S möglich. Aufgrund des komplexen Primer-Designs und der hohen Wahrscheinlichkeit unspezifischer Amplifikation in der LAMP wurde eine neue Bst DNA-Polymerase-abhängige isothermale Amplifikationsreaktion entwickelt. Durch die Integration einer spezifischen Linkerstruktur (abasische Stelle oder Hexaethylenglykol) zwischen zwei Primersequenzen konnte ein bifunktioneller Primer die effiziente Regenerierung der Primerbindungsstellen gewährleisten. Der neue Primer induziert nach der spezifischen Hybridisierung auf dem Templat die Rückfaltung zu einer Haarnadelstruktur und blockiert gleichzeitig die Polymeraseaktivität am Gegenstrang, wodurch eine autozyklische Amplifikation trotz konstanter Reaktionstemperatur möglich ist. Die Effizienz der „Hinge-initiated Primer dependent Amplification“ (HIP) konnte abschließend durch die Verkürzung der Distanz zwischen einem modifizierten Hinge-Primer und einem PCR-ähnlichen Primer verbessert werden.
Schlussfolgerung: Die LAMP hat sich aufgrund der hohen Robustheit und Effizienz zu einer leistungsfähigen Alternative für die klassische PCR in der molekularbiologischen Diagnostik entwickelt. Unterschiedliche Detektionsverfahren verbessern die Leistungsfähigkeit der qualitativen und quantitativen LAMP für die Feldanwendungen und für die Diagnostik, da die neuen DNA- und Pyrophosphat-abhängigen Nachweismethoden in einer geschlossenen Reaktion eingesetzt werden können und so eine einfache Pathogendiagnostik ermöglichen. Die gezeigten Methoden können darüber hinaus zu einer Kostensenkung und Zeitersparnis gegenüber den herkömmlichen Methoden beitragen. Ein attraktives Ziel stellt die Weiterentwicklung der HIP für den Pathogennachweis als Alternative zur LAMP dar. Hierbei können die neuen LAMP-Detektionsverfahren ebenfalls Anwendung finden. Die Verwendung von Bst DNA-Polymerase-abhängigen Reaktionen ermöglicht darüber hinaus die Integration einer robusten isothermalen Amplifikation in mikrofluidische Systeme. Durch die Kombination der Probenvorbereitung, Amplifikation und Detektion sind zukünftige Anwendungen mit kurzer Analysezeit und geringem apparativen Aufwand insbesondere in der Pathogendiagnostik möglich.
Magnetische Eisenoxidnanopartikel werden bereits seit geraumer Zeit erfolgreich als MRT-Kontrastmittel in der klinischen Bildgebung eingesetzt. Durch Optimierung der magnetischen Eigenschaften der Nanopartikel kann die Aussagekraft von MR-Aufnahmen verbessert und somit der diagnostische Wert einer MR-Anwendung weiter erhöht werden. Neben der Verbesserung bestehender Verfahren wird die bildgebende Diagnostik ebenso durch die Entwicklung neuer Verfahren, wie dem Magnetic Particle Imaging, vorangetrieben. Da hierbei das Messsignal von den magnetischen Nanopartikeln selbst erzeugt wird, birgt das MPI einen enormen Vorteil hinsichtlich der Sensitivität bei gleichzeitig hoher zeitlicher und räumlicher Auflösung. Da es aktuell jedoch keinen kommerziell vertriebenen in vivo-tauglichen MPI-Tracer gibt, besteht ein dringender Bedarf an geeigneten innovativen Tracermaterialien. Daraus resultierte die Motivation dieser Arbeit biokompatible und superparamagnetische Eisenoxidnanopartikel für den Einsatz als in vivo-Diagnostikum insbesondere im Magnetic Particle Imaging zu entwickeln. Auch wenn der Fokus auf der Tracerentwicklung für das MPI lag, wurde ebenso die MR-Performance bewertet, da geeignete Partikel somit alternativ oder zusätzlich als MR-Kontrastmittel mit verbesserten Kontrasteigenschaften eingesetzt werden könnten.
Die Synthese der Eisenoxidnanopartikel erfolgte über die partielle Oxidation von gefälltem Eisen(II)-hydroxid und Green Rust sowie eine diffusionskontrollierte Kopräzipitation in einem Hydrogel.
Mit der partiellen Oxidation von Eisen(II)-hydroxid und Green Rust konnten erfolgreich biokompatible und über lange Zeit stabile Eisenoxidnanopartikel synthetisiert werden. Zudem wurden geeignete Methoden zur Formulierung und Sterilisierung etabliert, wodurch zahlreiche Voraussetzungen für eine Anwendung als in vivo-Diagnostikum geschaffen wurden. Weiterhin ist auf Grundlage der MPS-Performance eine hervorragende Eignung dieser Partikel als MPI-Tracer zu erwarten, wodurch die Weiterentwicklung der MPI-Technologie maßgeblich vorangetrieben werden könnte. Die Bestimmung der NMR-Relaxivitäten sowie ein initialer in vivo-Versuch zeigten zudem das große Potential der formulierten Nanopartikelsuspensionen als MRT-Kontrastmittel. Die Modifizierung der Partikeloberfläche ermöglicht ferner die Herstellung zielgerichteter Nanopartikel sowie die Markierung von Zellen, wodurch das mögliche Anwendungsspektrum maßgeblich erweitert wurde.
Im zweiten Teil wurden Partikel durch eine diffusionskontrollierte Kopräzipitation im Hydrogel, wobei es sich um eine bioinspirierte Modifikation der klassischen Kopräzipitation handelt, synthetisiert, wodurch Partikel mit einer durchschnittlichen Kristallitgröße von 24 nm generiert werden konnten. Die Bestimmung der MPS- und MR-Performance elektrostatisch stabilisierter Partikel ergab vielversprechende Resultate. In Vorbereitung auf die Entwicklung eines in vivo-Diagnostikums wurden die Partikel anschließend erfolgreich sterisch stabilisiert, wodurch der kolloidale Zustand in MilliQ-Wasser über lange Zeit aufrechterhalten werden konnte. Durch Zentrifugation konnten die Partikel zudem erfolgreich in verschiedene Größenfraktionen aufgetrennt werden. Dies ermöglichte die Bestimmung der idealen Aggregatgröße dieses Partikelsystems in Bezug auf die MPS-Performance.
Thermal cis-trans isomerization of azobenzene studied by path sampling and QM/MM stochastic dynamics
(2017)
Azobenzene-based molecular photoswitches have extensively been applied to biological systems, involving photo-control of peptides, lipids and nucleic acids. The isomerization between the stable trans and the metastable cis state of the azo moieties leads to pronounced changes in shape and other physico-chemical properties of the molecules into which they are incorporated. Fast switching can be induced via transitions to excited electronic states and fine-tuned by a large number of different substituents at the phenyl rings. But a rational design of tailor-made azo groups also requires control of their stability in the dark, the half-lifetime of the cis isomer. In computational chemistry, thermally activated barrier crossing on the ground state Born-Oppenheimer surface can efficiently be estimated with Eyring’s transition state theory (TST) approach; the growing complexity of the azo moiety and a rather heterogeneous environment, however, may render some of the underlying simplifying assumptions problematic.
In this dissertation, a computational approach is established to remove two restrictions at once: the environment is modeled explicitly by employing a quantum mechanical/molecular mechanics (QM/MM) description; and the isomerization process is tracked by analyzing complete dynamical pathways between stable states. The suitability of this description is validated by using two test systems, pure azo benzene and a derivative with electron donating and electron withdrawing substituents (“push-pull” azobenzene). Each system is studied in the gas phase, in toluene and in polar DMSO solvent. The azo molecules are treated at the QM level using a very recent, semi-empirical approximation to density functional theory (density functional tight binding approximation). Reactive pathways are sampled by implementing a version of the so-called transition path sampling method (TPS), without introducing any bias into the system dynamics. By analyzing ensembles of reactive trajectories, the change in isomerization pathway from linear inversion to rotation in going from apolar to polar solvent, predicted by the TST approach, could be verified for the push-pull derivative. At the same time, the mere presence of explicit solvation is seen to broaden the distribution of isomerization pathways, an effect TST cannot account for.
Using likelihood maximization based on the TPS shooting history, an improved reaction coordinate was identified as a sine-cosine combination of the central bend angles and the rotation dihedral, r (ω,α,α′). The computational van’t Hoff analysis for the activation entropies was performed to gain further insight into the differential role of solvent for the case of the unsubstituted and the push-pull azobenzene. In agreement with the experiment, it yielded positive activation entropies for azobenzene in the DMSO solvent while negative for the push-pull derivative, reflecting the induced ordering of solvent around the more dipolar transition state associated to the latter compound. Also, the dynamically corrected rate constants were evaluated using the reactive flux approach where an increase comparable to the experimental one was observed for a high polarity medium for both azobenzene derivatives.
Nowadays, graph data models are employed, when relationships between entities have to be stored and are in the scope of queries. For each entity, this graph data model locally stores relationships to adjacent entities. Users employ graph queries to query and modify these entities and relationships. These graph queries employ graph patterns to lookup all subgraphs in the graph data that satisfy certain graph structures. These subgraphs are called graph pattern matches. However, this graph pattern matching is NP-complete for subgraph isomorphism. Thus, graph queries can suffer a long response time, when the number of entities and relationships in the graph data or the graph patterns increases.
One possibility to improve the graph query performance is to employ graph views that keep ready graph pattern matches for complex graph queries for later retrieval. However, these graph views must be maintained by means of an incremental graph pattern matching to keep them consistent with the graph data from which they are derived, when the graph data changes. This maintenance adds subgraphs that satisfy a graph pattern to the graph views and removes subgraphs that do not satisfy a graph pattern anymore from the graph views.
Current approaches for incremental graph pattern matching employ Rete networks. Rete networks are discrimination networks that enumerate and maintain all graph pattern matches of certain graph queries by employing a network of condition tests, which implement partial graph patterns that together constitute the overall graph query. Each condition test stores all subgraphs that satisfy the partial graph pattern. Thus, Rete networks suffer high memory consumptions, because they store a large number of partial graph pattern matches. But, especially these partial graph pattern matches enable Rete networks to update the stored graph pattern matches efficiently, because the network maintenance exploits the already stored partial graph pattern matches to find new graph pattern matches. However, other kinds of discrimination networks exist that can perform better in time and space than Rete networks. Currently, these other kinds of networks are not used for incremental graph pattern matching.
This thesis employs generalized discrimination networks for incremental graph pattern matching. These discrimination networks permit a generalized network structure of condition tests to enable users to steer the trade-off between memory consumption and execution time for the incremental graph pattern matching. For that purpose, this thesis contributes a modeling language for the effective definition of generalized discrimination networks. Furthermore, this thesis contributes an efficient and scalable incremental maintenance algorithm, which updates the (partial) graph pattern matches that are stored by each condition test. Moreover, this thesis provides a modeling evaluation, which shows that the proposed modeling language enables the effective modeling of generalized discrimination networks. Furthermore, this thesis provides a performance evaluation, which shows that a) the incremental maintenance algorithm scales, when the graph data becomes large, and b) the generalized discrimination network structures can outperform Rete network structures in time and space at the same time for incremental graph pattern matching.
With Saccharomyces cerevisiae being a commonly used host organism for synthetic biology and biotechnology approaches, the work presented here aims at the development of novel tools to improve and facilitate pathway engineering and heterologous protein production in yeast. Initially, the multi-part assembly strategy AssemblX was established, which allows the fast, user-friendly and highly efficient construction of up to 25 units, e.g. genes, into a single DNA construct. To speed up complex assembly projects, starting from sub-gene fragments and resulting in mini-chromosome sized constructs, AssemblX follows a level-based approach: Level 0 stands for the assembly of genes from multiple sub-gene fragments; Level 1 for the combination of up to five Level 0 units into one Level 1 module; Level 2 for linkages of up to five Level 1 modules into one Level 2 module. This way, all Level 0 and subsequently all Level 1 assemblies can be carried out simultaneously. Individually planned, overlap-based Level 0 assemblies enable scar-free and sequence-independent assemblies of transcriptional units, without limitations in fragment number, size or content. Level 1 and Level 2 assemblies, which are carried out via predefined, computationally optimized homology regions, follow a standardized, highly efficient and PCR-free scheme. AssemblX follows a virtually sequence-independent scheme with no need for time-consuming domestication of assembly parts. To minimize the risk of human error and to facilitate the planning of assembly projects, especially for individually designed Level 0 constructs, the whole AssemblX process is accompanied by a user-friendly webtool. This webtool provides the user with an easy-to-use operating surface and returns a bench-protocol including all cloning steps. The efficiency of the assembly process is further boosted through the implementation of different features, e.g. ccdB counter selection and marker switching/reconstitution. Due to the design of homology regions and vector backbones the user can flexibly choose between various overlap-based cloning methods, enabling cost-efficient assemblies which can be carried out either in E. coli or yeast. Protein production in yeast is additionally supported by a characterized library of 40 constitutive promoters, fully integrated into the AssemblX toolbox. This provides the user with a starting point for protein balancing and pathway engineering. Furthermore, the final assembly cassette can be subcloned into any vector, giving the user the flexibility to transfer the individual construct into any host organism different from yeast.
As successful production of heterologous compounds generally requires a precise adjustment of protein levels or even manipulation of the host genome to e.g. inhibit unwanted feedback regulations, the optogenetic transcriptional regulation tool PhiReX was designed. In recent years, light induction was reported to enable easy, reversible, fast, non-toxic and nearly gratuitous regulation, thereby providing manifold advantages compared to conventional chemical inducers. The optogenetic interface established in this study is based on the photoreceptor PhyB and its interacting protein PIF3. Both proteins, derived from Arabidopsis thaliana, dimerize in a red/far-red light-responsive manner. This interaction depends on a chromophore, naturally not available in yeast. By fusing split proteins to both components of the optical dimerizer, active enzymes can be reconstituted in a light-dependent manner. For the construction of the red/far-red light sensing gene expression system PhiReX, a customizable synTALE-DNA binding domain was fused to PhyB, and a VP64 activation domain to PIF3. The synTALE-based transcription factor allows programmable targeting of any desired promoter region. The first, plasmid-based PhiReX version mediates chromophore- and light-dependent expression of the reporter gene, but required further optimization regarding its robustness, basal expression and maximum output. This was achieved by genome-integration of the optical regulator pair, by cloning the reporter cassette on a high-copy plasmid and by additional molecular modifications of the fusion proteins regarding their cellular localization. In combination, this results in a robust and efficient activation of cells over an incubation time of at least 48 h. Finally, to boost the potential of PhiReX for biotechnological applications, yeast was engineered to produce the chromophore. This overcomes the need to supply the expensive and photo-labile compound exogenously. The expression output mediated through PhiReX is comparable to the strong constitutive yeast TDH3 promoter and - in the experiments described here - clearly exceeds the commonly used galactose inducible GAL1 promoter.
The fast-developing field of synthetic biology enables the construction of complete synthetic genomes. The upcoming Synthetic Yeast Sc2.0 Project is currently underway to redesign and synthesize the S. cerevisiae genome. As a prerequisite for the so-called “SCRaMbLE” system, all Sc2.0 chromosomes incorporate symmetrical target sites for Cre recombinase (loxPsym sites), enabling rearrangement of the yeast genome after induction of Cre with the toxic hormonal substance beta-estradiol. To overcome the safety concern linked to the use of beta-estradiol, a red light-inducible Cre recombinase, dubbed L-SCRaMbLE, was established in this study. L-SCRaMbLE was demonstrated to allow a time- and chromophore-dependent recombination with reliable off-states when applied to a plasmid containing four genes of the beta-carotene pathway, each flanked with loxPsym sites. When directly compared to the original induction system, L-SCRaMbLE generates a larger variety of recombination events and lower basal activity. In conclusion, L-SCRaMbLE provides a promising and powerful tool for genome rearrangement.
The three tools developed in this study provide so far unmatched possibilities to tackle complex synthetic biology projects in yeast by addressing three different stages: fast and reliable biosynthetic pathway assembly; highly specific, orthogonal gene regulation; and tightly controlled synthetic evolution of loxPsym-containing DNA constructs.
The functioning of the surface water-groundwater interface as buffer, filter and reactive zone is important for water quality, ecological health and resilience of streams and riparian ecosystems. Solute and heat exchange across this interface is driven by the advection of water. Characterizing the flow conditions in the streambed is challenging as flow patterns are often complex and multidimensional, driven by surface hydraulic gradients and groundwater discharge. This thesis presents the results of an integrated approach of studies, ranging from the acquisition of field data, the development of analytical and numerical approaches to analyse vertical temperature profiles to the detailed, fully-integrated 3D numerical modelling of water and heat flux at the reach scale. All techniques were applied in order to characterize exchange flux between stream and groundwater, hyporheic flow paths and temperature patterns.
The study was conducted at a reach-scale section of the lowland Selke River, characterized by distinctive pool riffle sequences and fluvial islands and gravel bars. Continuous time series of hydraulic heads and temperatures were measured at different depths in the river bank, the hyporheic zone and within the river. The analyses of the measured diurnal temperature variation in riverbed sediments provided detailed information about the exchange flux between river and groundwater. Beyond the one-dimensional vertical water flow in the riverbed sediment, hyporheic and parafluvial flow patterns were identified. Subsurface flow direction and magnitude around fluvial islands and gravel bars at the study site strongly depended on the position around the geomorphological structures and on the river stage. Horizontal water flux in the streambed substantially impacted temperature patterns in the streambed. At locations with substantial horizontal fluxes the penetration depths of daily temperature fluctuations was reduced in comparison to purely vertical exchange conditions.
The calibrated and validated 3D fully-integrated model of reach-scale water and heat fluxes across the river-groundwater interface was able to accurately represent the real system. The magnitude and variations of the simulated temperatures matched the observed ones, with an average mean absolute error of 0.7 °C and an average Nash Sutcliffe Efficiency of 0.87. The simulation results showed that the water and heat exchange at the surface water-groundwater interface is highly variable in space and time with zones of daily temperature oscillations penetrating deep into the sediment and spots of daily constant temperature following the average groundwater temperature. The average hyporheic flow path temperature was found to strongly correlate with the flow path residence time (flow path length) and the temperature gradient between river and groundwater. Despite the complexity of these processes, the simulation results allowed the derivation of a general empirical relationship between the hyporheic residence times and temperature patterns. The presented results improve our understanding of the complex spatial and temporal dynamics of water flux and thermal processes within the shallow streambed. Understanding these links provides a general basis from which to assess hyporheic temperature conditions in river reaches.
In this thesis, stochastic dynamics modelling collective motions of populations, one of the most mysterious type of biological phenomena, are considered. For a system of N particle-like individuals, two kinds of asymptotic behaviours are studied : ergodicity and flocking properties, in long time, and propagation of chaos, when the number N of agents goes to infinity. Cucker and Smale, deterministic, mean-field kinetic model for a population without a hierarchical structure is the starting point of our journey : the first two chapters are dedicated to the understanding of various stochastic dynamics it inspires, with random noise added in different ways. The third chapter, an attempt to improve those results, is built upon the cluster expansion method, a technique from statistical mechanics. Exponential ergodicity is obtained for a class of non-Markovian process with non-regular drift. In the final part, the focus shifts onto a stochastic system of interacting particles derived from Keller and Segel 2-D parabolicelliptic model for chemotaxis. Existence and weak uniqueness are proven.
Das Thema der vorliegenden Arbeit ist die semantische Suche im Kontext heutiger Informationsmanagementsysteme. Zu diesen Systemen zählen Intranets, Web 3.0-Anwendungen sowie viele Webportale, die Informationen in heterogenen Formaten und Strukturen beinhalten. Auf diesen befinden sich einerseits Daten in strukturierter Form und andererseits Dokumente, die inhaltlich mit diesen Daten in Beziehung stehen. Diese Dokumente sind jedoch in der Regel nur teilweise strukturiert oder vollständig unstrukturiert. So beschreiben beispielsweise Reiseportale durch strukturierte Daten den Zeitraum, das Reiseziel, den Preis einer Reise und geben in unstrukturierter Form weitere Informationen, wie Beschreibungen zum Hotel, Zielort, Ausflugsziele an.
Der Fokus heutiger semantischer Suchmaschinen liegt auf dem Finden von Wissen entweder in strukturierter Form, auch Faktensuche genannt, oder in semi- bzw. unstrukturierter Form, was üblicherweise als semantische Dokumentensuche bezeichnet wird. Einige wenige Suchmaschinen versuchen die Lücke zwischen diesen beiden Ansätzen zu schließen. Diese durchsuchen zwar gleichzeitig strukturierte sowie unstrukturierte Daten, werten diese jedoch entweder weitgehend voneinander unabhängig aus oder schränken die Suchmöglichkeiten stark ein, indem sie beispielsweise nur bestimmte Fragemuster unterstützen. Hierdurch werden die im System verfügbaren Informationen nicht ausgeschöpft und gleichzeitig unterbunden, dass Zusammenhänge zwischen einzelnen Inhalten der jeweiligen Informationssysteme und sich ergänzende Informationen den Benutzer erreichen.
Um diese Lücke zu schließen, wurde in der vorliegenden Arbeit ein neuer hybrider semantischer Suchansatz entwickelt und untersucht, der strukturierte und semi- bzw. unstrukturierte Inhalte während des gesamten Suchprozesses kombiniert. Durch diesen Ansatz werden nicht nur sowohl Fakten als auch Dokumente gefunden, es werden auch Zusammenhänge, die zwischen den unterschiedlich strukturierten Daten bestehen, in jeder Phase der Suche genutzt und fließen in die Suchergebnisse mit ein. Liegt die Antwort zu einer Suchanfrage nicht vollständig strukturiert, in Form von Fakten, oder unstrukturiert, in Form von Dokumenten vor, so liefert dieser Ansatz eine Kombination der beiden. Die Berücksichtigung von unterschiedlich Inhalten während des gesamten Suchprozesses stellt jedoch besondere Herausforderungen an die Suchmaschine. Diese muss in der Lage sein, Fakten und Dokumente in Abhängigkeit voneinander zu durchsuchen, sie zu kombinieren sowie die unterschiedlich strukturierten Ergebnisse in eine geeignete Rangordnung zu bringen. Weiterhin darf die Komplexität der Daten nicht an die Endnutzer weitergereicht werden. Die Darstellung der Inhalte muss vielmehr sowohl bei der Anfragestellung als auch bei der Darbietung der Ergebnisse verständlich und leicht interpretierbar sein.
Die zentrale Fragestellung der Arbeit ist, ob ein hybrider Ansatz auf einer vorgegebenen Datenbasis die Suchanfragen besser beantworten kann als die semantische Dokumentensuche und die Faktensuche für sich genommen, bzw. als eine Suche die diese Ansätze im Rahmen des Suchprozesses nicht kombiniert. Die durchgeführten Evaluierungen aus System- und aus Benutzersicht zeigen, dass die im Rahmen der Arbeit entwickelte hybride semantische Suchlösung durch die Kombination von strukturierten und unstrukturierten Inhalten im Suchprozess bessere Antworten liefert als die oben genannten Verfahren und somit Vorteile gegenüber bisherigen Ansätzen bietet. Eine Befragung von Benutzern macht deutlich, dass die hybride semantische Suche als verständlich empfunden und für heterogen strukturierte Datenmengen bevorzugt wird.
Estuarine marshes are ecosystems that are situated at the transition zone between land and water and are thus controlled by physical and biological interactions. Marsh vegetation offers important ecosystem services by filtrating solid and dissolved substances from the water and providing habitat. By buffering a large part of the arriving flow velocity, attenuating wave energy and serving as erosion control for riverbanks, tidal marshes furthermore reduce the destructive effects of storm surges and storm waves and thus contribute to ecosystem-based shore protection. However, in many estuaries, extensive embankments, artificial bank protection, river dredging and agriculture threaten tidal marshes. Global warming might entail additional risks, such as changes in water levels, an increase of the tidal amplitude and a resulting shift of the salinity zones. This can affect the dynamics of the shore and foreland vegetation, and vegetation belts can be narrowed or fragmented. Against this background, it is crucial to gain a better understanding of the processes underlying the spatio temporal vegetation dynamics in brackish marshes. Furthermore, a better understanding of how plant-habitat relationships generate patterns in tidal marsh vegetation is vital to maintain ecosystem functions and assess the response of marshes to environmental change as well as the success of engineering and restoration projects.
For this purpose, three research objectives were addressed within this thesis: (1) to explore the possibility of vegetation serving as self-adaptive shore protection by quantifying the reduction of current velocity in the vegetation belt and the morphologic plasticity of a brackish marsh pioneer, (2) to disentangle the roles of abiotic factors and interspecific competition on species distribution and stand characteristics in brackish marshes, and (3) to develop a mechanistic vegetation model that helps analysing the influence of habitat conditions on the spatio-temporal dynamic of tidal marsh vegetation. These aspects were investigated using a combination of field studies and statistical as well as process-based modelling.
To explore the possibility of vegetation serving as self-adaptive coastal protection, in the first study, we measured current velocity with and without living vegetation, recorded ramet density and plant thickness during two growing periods at two locations in the Elbe estuary and assessed the adaptive value of a larger stem diameter of plants at locations with higher mechanical stress by biomechanical measurements. The results of this study show that under non-storm conditions, the vegetation belt of the marsh pioneer Bolboschoenus maritimus is able to buffer a large proportion of the flow velocity. We were furthermore able to show that morphological traits of plant species are adapted to hydrodynamic forces by demonstrating a positive correlation between ramet thickness and cross-shore current. In addition, our measurements revealed that thicker ramets growing at the front of the vegetation belt have a significantly higher stability than ramets inside the vegetation belt. This self-adaptive effect improves the ability of B. maritimus to grow and persist in the pioneer zone and could provide an adaptive value in habitats with high mechanical stress.
In the second study, we assessed the distribution of the two marsh species and a set of stand characteristics, namely aboveground and belowground biomass, ramet density, ramet height and the percentage of flowering ramets. Furthermore, we collected information on several abiotic habitat factors to test their effect on plant growth and zonation with generalised linear models (GLMs). Our results demonstrate that flow velocity is the main factor controlling the distribution of Bolboschoenus maritimus and Phragmites australis. Additionally, inundation height and duration, as well as intraspecific competition affect distribution patterns. This study furthermore shows that cross-shore flow velocity does not only directly influence the distribution of the two marsh species, but also alters the plants’ occurrence relative to inun-dation height and duration. This suggests an effect of cross-shore flow velocity on their tolerance to inundation. The analysis of the measured stand characteristics revealed a negative effect of total flow velocity on all measured parameters of B. maritimus and thus confirmed our expectation that flow velocity is a decisive stressor which influences the growth of this species.
To gain a better understanding of the processes and habitat factors influencing the spatio-temporal vegetation dynamics in brackish marshes, I built a spatially explicit, mechanistic model applying a pattern-oriented modelling approach. A sensitivity analysis of the para-meters of this dynamic habitat-macrophyte model HaMac suggests that rhizome growth is the key process for the lateral dynamics of brackish marshes. From the analysed habitat factors, P. australis patterns were mainly influenced by flow velocity. The competition with P. australis was of key importance for the belowground biomass of B. maritimus. Concerning vegetation dynamics, the model results emphasise that without the effect of flow velocity the B. maritimus vegetation belt would expand into the tidal flat at locations with present vegetation recession, suggesting that flow velocity is the main reason for vegetation recession at exposed locations.
Overall, the results of this thesis demonstrate that brackish marsh vegetation considerably contributes to flow reduction under average flow conditions and can hence be a valuable component of shore-protection schemes. At the same time, the distribution, growth and expansion of tidal marsh vegetation is substantially influenced by flow. Altogether, this thesis provides a clear step forward in understanding plant-habitat interactions in tidal marshes. Future research should integrate studies of vertical marsh accretion with research on the factors that control the lateral position of marshes.
Information on the contemporary in-situ stress state of the earth’s crust is essential for geotechnical applications and physics-based seismic hazard assessment. Yet, stress data records for a data point are incomplete and their availability is usually not dense enough to allow conclusive statements. This demands a thorough examination of the in-situ stress field which is achieved by 3D geomechanicalnumerical models. However, the models spatial resolution is limited and the resulting local stress state is subject to large uncertainties that confine the significance of the findings. In addition, temporal variations of the in-situ stress field are naturally or anthropogenically induced. In my thesis I address these challenges in three manuscripts that investigate (1) the current crustal stress field orientation, (2) the 3D geomechanical-numerical modelling of the in-situ stress state, and (3) the phenomenon of injection induced temporal stress tensor rotations. In the first manuscript I present the first comprehensive stress data compilation of Iceland with 495 data records. Therefore, I analysed image logs from 57 boreholes in Iceland for indicators of the orientation of the maximum horizontal stress component. The study is the first stress survey from different kinds of stress indicators in a geologically very young and tectonically active area of an onshore spreading ridge. It reveals a distinct stress field with a depth independent stress orientation even very close to the spreading centre. In the second manuscript I present a calibrated 3D geomechanical-numerical modelling approach of the in-situ stress state of the Bavarian Molasse Basin that investigates the regional (70x70x10km³) and local (10x10x10km³) stress state. To link these two models I develop a multi-stage modelling approach that provides a reliable and efficient method to derive from the larger scale model initial and boundary conditions for the smaller scale model. Furthermore, I quantify the uncertainties in the models results which are inherent to geomechanical-numerical modelling in general and the multi-stage approach in particular. I show that the significance of the models results is mainly reduced due to the uncertainties in the material properties and the low number of available stress magnitude data records for calibration. In the third manuscript I investigate the phenomenon of injection induced temporal stress tensor rotation and its controlling factors. I conduct a sensitivity study with a 3D generic thermo-hydro-mechanical model. I show that the key control factors for the stress tensor rotation are the permeability as the decisive factor, the injection rate, and the initial differential stress. In particular for enhanced geothermal systems with a low permeability large rotations of the stress tensor are indicated. According to these findings the estimation of the initial differential stress in a reservoir is possible provided the permeability is known and the angle of stress rotation is observed. I propose that the stress tensor rotations can be a key factor in terms of the potential for induced seismicity on pre-existing faults due to the reorientation of the stress field that changes the optimal orientation of faults.
The existence of diverse and active microbial ecosystems in the deep subsurface – a biosphere that was originally considered devoid of life – was discovered in multiple microbiological studies. However, most of the studies are restricted to marine ecosystems, while our knowledge about the microbial communities in the deep subsurface of lake systems and their potentials to adapt to changing environmental conditions is still fragmentary. This doctoral thesis aims to build up a unique data basis for providing the first detailed high-throughput characterization of the deep biosphere of lacustrine sediments and to emphasize how important it is to differentiate between the living and the dead microbial community in deep biosphere studies.
In this thesis, up to 3.6 Ma old sediments (up to 317 m deep) of the El’gygytgyn Crater Lake were examined, which represents the oldest terrestrial climate record of the Arctic. Combining next generation sequencing with detailed geochemical characteristics and other environmental parameters, the microbial community composition was analyzed in regard to changing climatic conditions within the last 3.6 Ma to 1.0 Ma (Pliocene and Pleistocene). DNA from all investigated sediments was successfully extracted and a surprisingly diverse (6,910 OTUs) and abundant microbial community in the El’gygytgyn deep sediments were revealed. The bacterial abundance (10³-10⁶ 16S rRNA copies g⁻¹ sediment) was up to two orders of magnitudes higher than the archaeal abundance (10¹-10⁵) and fluctuates with the Pleistocene glacial/interglacial cyclicality. Interestingly, a strong increase in the microbial diversity with depth was observed (approximately 2.5 times higher diversity in Pliocene sediments compared to Pleistocene sediments). The increase in diversity with depth in the Lake El’gygytgyn is most probably caused by higher sedimentary temperatures towards the deep sediment layers as well as an enhanced temperature-induced intra-lake bioproductivity and higher input of allochthonous organic-rich material during Pliocene climatic conditions. Moreover, the microbial richness parameters follow the general trends of the paleoclimatic parameters, such as the paleo-temperature and paleo-precipitation. The most abundant bacterial representatives in the El’gygytgyn deep biosphere are affiliated with the phyla Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria, which are also commonly distributed in the surrounding permafrost habitats. The predominated taxon was the halotolerant genus Halomonas (in average 60% of the total reads per sample).
Additionally, this doctoral thesis focuses on the live/dead differentiation of microbes in cultures and environmental samples. While established methods (e.g., fluorescence in situ hybridization, RNA analyses) are not applicable to the challenging El’gygytgyn sediments, two newer methods were adapted to distinguish between DNA from live cells and free (extracellular, dead) DNA: the propidium monoazide (PMA) treatment and the cell separation adapted for low amounts of DNA. The applicability of the DNA-intercalating dye PMA was successfully evaluated to mask free DNA of different cultures of methanogenic archaea, which play a major role in the global carbon cycle. Moreover, an optimal procedure to simultaneously treat bacteria and archaea was developed using 130 µM PMA and 5 min of photo-activation with blue LED light, which is also applicable on sandy environmental samples with a particle load of ≤ 200 mg mL⁻¹. It was demonstrated that the soil texture has a strong influence on the PMA treatment in particle-rich samples and that in particular silt and clay-rich samples (e.g., El’gygytgyn sediments) lead to an insufficient shielding of free DNA by PMA. Therefore, a cell separation protocol was used to distinguish between DNA from live cells (intracellular DNA) and extracellular DNA in the El’gygytgyn sediments. While comparing these two DNA pools with a total DNA pool extracted with a commercial kit, significant differences in the microbial composition of all three pools (mean distance of relative abundance: 24.1%, mean distance of OTUs: 84.0%) was discovered. In particular, the total DNA pool covers significantly fewer taxa than the cell-separated DNA pools and only inadequately represents the living community. Moreover, individual redundancy analyses revealed that the microbial community of the intra- and extracellular DNA pool are driven by different environmental factors. The living community is mainly influenced by life-dependent parameters (e.g., sedimentary matrix, water availability), while the extracellular DNA is dependent on the biogenic silica content. The different community-shaping parameters and the fact, that a redundancy analysis of the total DNA pool explains significantly less variance of the microbial community, indicate that the total DNA represents a mixture of signals of the live and dead microbial community.
This work provides the first fundamental data basis of the diversity and distribution of microbial deep biosphere communities of a lake system over several million years. Moreover, it demonstrates the substantial importance of extracellular DNA in old sediments. These findings may strongly influence future environmental community analyses, where applications of live/dead differentiation avoid incorrect interpretations due to a failed extraction of the living microbial community or an overestimation of the past community diversity in the course of total DNA extraction approaches.
We analyze an inverse noisy regression model under random design with the aim of estimating the unknown target function based on a given set of data, drawn according to some unknown probability distribution. Our estimators are all constructed by kernel methods, which depend on a Reproducing Kernel Hilbert Space structure using spectral regularization methods.
A first main result establishes upper and lower bounds for the rate of convergence under a given source condition assumption, restricting the class of admissible distributions. But since kernel methods scale poorly when massive datasets are involved, we study one example for saving computation time and memory requirements in more detail. We show that Parallelizing spectral algorithms also leads to minimax optimal rates of convergence provided the number of machines is chosen appropriately.
We emphasize that so far all estimators depend on the assumed a-priori smoothness of the target function and on the eigenvalue decay of the kernel covariance operator, which are in general unknown. To obtain good purely data driven estimators constitutes the problem of adaptivity which we handle for the single machine problem via a version of the Lepskii principle.
Background: Consumption of whole-grain, coffee, and red meat were consistently related to the risk of developing type 2 diabetes in prospective cohort studies, but potentially underlying biological mechanisms are not well understood. Metabolomics profiles were shown to be sensitive to these dietary exposures, and at the same time to be informative with respect to the risk of type 2 diabetes. Moreover, graphical network-models were demonstrated to reflect the biological processes underlying high-dimensional metabolomics profiles.
Aim: The aim of this study was to infer hypotheses on the biological mechanisms that link consumption of whole-grain bread, coffee, and red meat, respectively, to the risk of developing type 2 diabetes. More specifically, it was aimed to consider network models of amino acid and lipid profiles as potential mediators of these risk-relations.
Study population: Analyses were conducted in the prospective EPIC-Potsdam cohort (n = 27,548), applying a nested case-cohort design (n = 2731, including 692 incident diabetes cases). Habitual diet was assessed with validated semiquantitative food-frequency questionnaires. Concentrations of 126 metabolites (acylcarnitines, phosphatidylcholines, sphingomyelins, amino acids) were determined in baseline-serum samples. Incident type 2 diabetes cases were assed and validated in an active follow-up procedure. The median follow-up time was 6.6 years.
Analytical design: The methodological approach was conceptually based on counterfactual causal inference theory. Observations on the network-encoded conditional independence structure restricted the space of possible causal explanations of observed metabolomics-data patterns. Given basic directionality assumptions (diet affects metabolism; metabolism affects future diabetes incidence), adjustment for a subset of direct neighbours was sufficient to consistently estimate network-independent direct effects. Further model-specification, however, was limited due to missing directionality information on the links between metabolites. Therefore, a multi-model approach was applied to infer the bounds of possible direct effects. All metabolite-exposure links and metabolite-outcome links, respectively, were classified into one of three categories: direct effect, ambiguous (some models indicated an effect others not), and no-effect.
Cross-sectional and longitudinal relations were evaluated in multivariable-adjusted linear regression and Cox proportional hazard regression models, respectively. Models were comprehensively adjusted for age, sex, body mass index, prevalence of hypertension, dietary and lifestyle factors, and medication.
Results: Consumption of whole-grain bread was related to lower levels of several lipid metabolites with saturated and monounsaturated fatty acids. Coffee was related to lower aromatic and branched-chain amino acids, and had potential effects on the fatty acid profile within lipid classes. Red meat was linked to lower glycine levels and was related to higher circulating concentrations of branched-chain amino acids. In addition, potential marked effects of red meat consumption on the fatty acid composition within the investigated lipid classes were identified.
Moreover, potential beneficial and adverse direct effects of metabolites on type 2 diabetes risk were detected. Aromatic amino acids and lipid metabolites with even-chain saturated (C14-C18) and with specific polyunsaturated fatty acids had adverse effects on type 2 diabetes risk. Glycine, glutamine, and lipid metabolites with monounsaturated fatty acids and with other species of polyunsaturated fatty acids were classified as having direct beneficial effects on type 2 diabetes risk.
Potential mediators of the diet-diabetes links were identified by graphically overlaying this information in network models. Mediation analyses revealed that effects on lipid metabolites could potentially explain about one fourth of the whole-grain bread effect on type 2 diabetes risk; and that effects of coffee and red meat consumption on amino acid and lipid profiles could potentially explain about two thirds of the altered type 2 diabetes risk linked to these dietary exposures.
Conclusion: An algorithm was developed that is capable to integrate single external variables (continuous exposures, survival time) and high-dimensional metabolomics-data in a joint graphical model. Application to the EPIC-Potsdam cohort study revealed that the observed conditional independence patterns were consistent with the a priori mediation hypothesis: Early effects on lipid and amino acid metabolism had the potential to explain large parts of the link between three of the most widely discussed diabetes-related dietary exposures and the risk of developing type 2 diabetes.
We present electrical impedance measurements of amoeboid cells on microelectrodes. The model organism Dictyostelium discoideum shows under starvation conditions a transition to collective behavior when chemotactic cells collect in multicellular aggregates. We show how impedance recordings give a precise picture of the stages of aggregation by tracing the dynamics of cell-substrate adhesion. Furthermore, we present for the first time systematic single cell measurements of wild type cells and four mutant strains that differ in their substrate adhesion strength. We recorded the projected cell area by time lapse microscopy and found a correlation between quasi-periodic oscillations in the kinetics of the projected area - the cell shape oscillation - and the long-term trend in the impedance signal. Typically, amoeboid motility advances via a cycle of membrane protrusion, substrate adhesion, traction of the cell body and tail retraction. This motility cycle results in the quasi-periodic oscillations of the projected cell area and the impedance. In all cell lines measured, similar periods were observed for this cycle, despite the differences in attachment strength. We observed that cell-substrate attachment strength strongly affects the impedance in that the deviations from mean (the magnitude of fluctuations) are enhanced in cells that effectively transmit forces, generated by the cytoskeleton, to the substrate. For example, in talA- cells, which lack the actin anchoring protein talin, the fluctuations are strongly reduced. Single cell force spectroscopy and results from a detachment assay, where adhesion is measured by exposing cells to shear stress, confirm that the magnitude of impedance fluctuations is a correct measure for the strength of substrate adhesion. Finally, we also worked on the integration of cell-substrate impedance sensors into microfluidic devices. A chip-based electrical chemotaxis assay is designed which measures the speed of chemotactic cells migrating over microelectrodes along a chemical concentration gradient.
During the course of millions of years, evolutionary forces have shaped the current distribution of species and their genetic variability, by influencing their phylogeny, adaptability and probability of survival. Southeast Asia is an extraordinary biodiverse region, where past climate events have resulted in dramatic changes in land availability and distribution of vegetation, resulting likewise in periodic connections between isolated islands and the mainland. These events have influenced the way species are distributed throughout this region but, more importantly, they influenced the genesis of genetic diversity. Despite the observation that a shared paleo-history resulted in very diverse species phylogeographic patterns, the mechanisms behind these patterns are still poorly understood.
In this thesis, I investigated and contrasted the phylogeography of three groups of ungulate species distributed within South and Southeast Asia, aiming to understand what mechanisms have shaped speciation and geographical distribution of genetic variability. For that purpose, I analysed the mitogenomes of historical samples, in order to account for populations from the entire range of species distributions – including populations that no longer exist. This thesis is organized in three manuscripts, which correspond to the three investigated groups: red muntjacs, Rusa deer and Asian rhinoceros.
Red muntjacs are a widely distributed species and occur in very different habitats. We found evidence for gene-flow among populations of different islands, indicative of their ability to utilize the available land corridors. However, we described also the existence of at least two dispersal barriers that created population differentiation within this group; one isolated Sundaic and Mainland populations and the second separated individuals from Sri Lanka.
Second, the two Rusa species investigated here revealed another consequence of the historical land connections. While the two species were monophyletic, we found evidence of hybridisation in Java, facilitated by the expansion of the widespread sambar, Rusa unicolor. Consequently, I found that all the individuals of Javan deer, R. timorensis which were transported to the east of Sundaland by humans, to be of hybrid descent.
In the last manuscript, we were able to include samples from the extinct mainland populations of both Sumatran and Javan rhinoceros. The results revealed a much higher genetic diversity of the historical populations than ever reported for the contemporaneous survivors. Their evolutionary histories revealed a close relationship to climatic events of the Pleistocene but, more importantly, point out the vast extent of genetic erosion within these two endangered species.
The specific phylogeographic history of the species showed some common patters of genetic differentiation that could be directly linked to the climatic and geological changes on the Sunda Shelf during the Pleistocene. However, by contrasting these results I discussed that the same geological events
did not always result in similar histories. One obvious example was the different permeability of the land corridors of Sundaland, as the ability of each species to utilize this newly available land was directly related to their specific ecological requirements. Taken together, these results have an important contribution to the general understanding of evolution in this biodiversity hotspot and the main drivers shaping the distribution of genetic diversity, but could also have important consequences for taxonomy and conservation of the three investigated groups.
Im Fokus der kumulativen Dissertationsschrift stehen Grundschullehrerinnen und Grundschullehrer in ihrer Rolle als Diagnostikerinnen und Diagnostiker. Exemplarisch werden mit der Einschätzung von Aufgabenschwierigkeiten und der Feststellung von Sprachförderbedarf zwei diagnostische Herausforderungen untersucht, die Lehrkräfte an Grundschulen bewältigen müssen.
Die vorliegende Arbeit umfasst drei empirische Teilstudien, die in einem Rahmentext integriert sind, in dem zunächst die theoretischen Hintergründe und die empirische Befundlage erläutert werden. Hierbei wird auf die diagnostische Kompetenz von Lehrkräften bzw. die Genauigkeit von Lehrerurteilen eingegangen. Ferner wird der Einsatz standardisierter Testinstrumente als wichtiger Bestandteil des diagnostischen Aufgabenfeldes von Lehrkräften charakterisiert. Außerdem werden zentrale Aspekte der Sprachdiagnostik in der Grundschule dargestellt.
In Teilstudie 1 (Hoffmann & Böhme, 2014b) wird der Frage nachgegangen, wie akkurat Grundschullehrerinnen und -lehrer die Schwierigkeit von Deutsch- und Mathematikaufgaben einschätzen. Darüber hinaus wird untersucht, welche Faktoren mit der Über- oder Unterschätzung der Schwierigkeit von Aufgaben zusammenhängen.
In Teilstudie 2 (Hoffmann & Böhme, 2017) wird geprüft, inwiefern die Klassifikationsgüte von Entschei¬dungen zum sprachlichen Förderbedarf mit den hierfür genutzten diagnostischen Informationsquellen kovariiert. Der Fokus liegt hierbei vor allem auf der Untersuchung von Effekten des Einsatzes von sprachdiagnostischen Verfahren.
Teilstudie 3 (Hoffmann, Böhme & Stanat, 2017) untersucht schließlich die Frage, welche diagnostischen Verfahren gegenwärtig bundesweit an den Grundschulen zur Feststellung sprachlichen Förderbedarfs genutzt werden und ob diese Verfahren etwa testtheoretischen Gütekriterien genügen.
Die zentralen Ergebnisse der Teilstudien werden im Rahmentext zusammen¬gefasst und studienübergreifend diskutiert. Hierbei wird auch auf methodische Stärken und Schwächen der drei Beiträge sowie auf Implikationen für die zukünftige Forschung und die schulische Praxis hingewiesen.
In der vorliegenden Arbeit konnten erfolgreich zwei unterschiedliche Hybridmaterialien (HM) über die Sol-Gel-Methode synthetisiert werden. Bei den HM handelt es sich um Monolithe mit einem Durchmesser von bis zu 4,5 cm. Das erste HM besteht aus Titandioxid und Bombyx mori Seide und wird als TS bezeichnet, während das zweite weniger Seide und zusätzlich Polyethylenoxid (PEO) enthält und daher als TPS abgekürzt wird. Einige der HM wurden nach der Synthese in eine wässrige Tetrachloridogoldsäure-Lösung getaucht, wodurch sich auf der Oberfläche Goldnanopartikel gebildet haben.
Die Materialien wurden mittels Elektronenmikroskopie, energiedispersiver Röntgenspektroskopie, Ramanspektroskopie sowie Röntgenpulverdiffraktometrie charakterisiert. Die Ergebnisse zeigen, dass beide HM aus etwa 5 nm großen, sphärischen Titandioxidnanopartikeln aufgebaut sind, die primär aus Anatas und zu einem geringen Anteil aus Brookit bestehen. Die Goldnanopartikel bei TPS_Au waren größer und polydisperser als die Goldnanopartikel auf dem TS_Au HM. Darüber hinaus sind die Goldnanopartikel im TS HM tiefer in das Material eingedrungen als beim TPS HM.
Die weiterführende Analyse der HM mittels Elementaranalyse und thermogravimetrischer Analyse ergab für TPS einen geringeren Anteil an organischen Bestandteilen im HM als für TS, obwohl für beide Synthesen die gleiche Masse an organischen Materialien eingesetzt wurde. Es wird vermutet, dass das PEO während der Synthese teilweise wieder aus dem Material herausgewaschen wird. Diese Theorie korreliert mit den Ergebnissen aus der Stickstoffsorption und der Quecksilberporosimetrie, die für das TPS HM eine höhere Oberfläche als für das TS HM anzeigten.
Die Variation einiger Syntheseparameter wie die Menge an Seide und PEO oder die Zusammensetzung der Titandioxidvorläuferlösung hatte einen großen Einfluss auf die synthetisierten HM. Während unterschiedliche Mengen an PEO die Größe des HM beeinflussten, konnte ohne Seide kein HM in einer ähnlichen Größe hergestellt werden. Die Bildung der HM wird stark von der Zusammensetzung der Titandioxidvorläuferlösung beeinflusst. Eine Veränderung führte daher nur selten zur Bildung eines homogenen HM.
Die in dieser Arbeit synthetisierten HM wurden als Photokatalysatoren für die Wasserspaltung und den Abbau von Methylenblau eingesetzt. Bei der photokatalytischen Wasserspaltung wurde zunächst der Einfluss unterschiedlicher Goldkonzentrationen beim TPS HM auf die Wasserstoffausbeute untersucht. Die besten Ergebnisse wurden bei einer Menge von 2,5 mg Tetrachloridogoldsäure erhalten. Darüber hinaus wurde gezeigt, dass mit dem TPS HM eine deutlich höhere Menge an Wasserstoff gewonnen werden konnte als mit dem TS HM. Die Ursachen für die schlechtere Aktivität werden in der geringeren spezifischen Oberfläche, der unterschiedlichen Porenstruktur, dem höheren Anteil an Seide und besonders in der geringeren Größe und höheren Eindringtiefe der Goldnanopartikel vermutet. Darüber hinaus konnte mit einem höheren UV-Anteil in der Lichtquelle sowie durch die Zugabe von Ethanol als Opferreagenz eine Zunahme der Wasserstoffausbeute erzielt werden.
Bei dem Methylenblauabbau wurde für beide HM zunächst nur eine Adsorption des Methylenblaus beobachtet. Nach der Zugabe von Wasserstoffperoxid konnte nach 8 h bereits eine fast vollständige Oxidation des Methylenblaus unter sichtbarem Licht beobachtet werden. Die Ursache für die etwas höhere Aktivität von TPS gegenüber TS wird in der unterschiedlichen Porenstruktur und dem höheren Anteil an Seide im TS HM vermutet. Insgesamt zeigen beide HM eine gute photokatalytische Aktivität für den Abbau von Methylenblau im Vergleich zu den erhaltenen Werten aus der Literatur.
To what extent cities can be made sustainable under the mega-trends of urbanization and climate change remains a matter of unresolved scientific debate. Our inability in answering this question lies partly in the deficient knowledge regarding pivotal humanenvironment interactions. Regarded as the most well documented anthropogenic climate modification, the urban heat island (UHI) effect – the warmth of urban areas relative to the rural hinterland – has raised great public health concerns globally. Worse still, heat waves are being observed and are projected to increase in both frequency and intensity, which further impairs the well-being of urban dwellers. Albeit with a substantial increase in the number of publications on UHI in the recent decades, the diverse urban-rural definitions applied in previous studies have remarkably hampered the general comparability of results achieved. In addition, few studies have attempted to synergize the land use data and thermal remote sensing to systematically assess UHI and its contributing factors.
Given these research gaps, this work presents a general framework to systematically quantify the UHI effect based on an automated algorithm, whereby cities are defined as clusters of maximum spatial continuity on the basis of land use data, with their rural hinterland being defined analogously. By combining land use data with spatially explicit surface skin temperatures from satellites, the surface UHI intensity can be calculated in a consistent and robust manner. This facilitates monitoring, benchmarking, and categorizing UHI intensities for cities across scales. In light of this innovation, the relationship between city size and UHI intensity has been investigated, as well as the contributions of urban form indicators to the UHI intensity.
This work delivers manifold contributions to the understanding of the UHI, which have complemented and advanced a number of previous studies. Firstly, a log-linear relationship between surface UHI intensity and city size has been confirmed among the 5,000 European cities. The relationship can be extended to a log-logistic one, when taking a wider range of small-sized cities into account. Secondly, this work reveals a complex interplay between UHI intensity and urban form. City size is found to have the strongest influence on the UHI intensity, followed by the fractality and the anisometry. However, their relative contributions to the surface UHI intensity depict a pronounced regional heterogeneity, indicating the importance of considering spatial patterns of UHI while implementing UHI adaptation measures.
Lastly, this work presents a novel seasonality of the UHI intensity for individual clusters in the form of hysteresis-like curves, implying a phase shift between the time series of UHI intensity and background temperatures. Combining satellite observation and urban boundary layer simulation, the seasonal variations of UHI are assessed from both screen and skin levels. Taking London as an example, this work ascribes the discrepancies between the seasonality observed at different levels mainly to the peculiarities of surface skin temperatures associated with the incoming solar radiation. In addition, the efforts in classifying cities according to their UHI characteristics highlight the important role of regional climates in determining the UHI.
This work serves as one of the first studies conducted to systematically and statistically scrutinize the UHI. The outcomes of this work are of particular relevance for the overall spatial planning and regulation at meso- and macro levels in order to harness the benefits of rapid urbanization, while proactively minimizing its ensuing thermal stress.
Underground coal gasification (UCG) has the potential to increase worldwide coal reserves by developing coal resources, currently not economically extractable by conventional mining methods. For that purpose, coal is combusted in situ to produce a high-calorific synthesis gas with different end-use options, including electricity generation as well as production of fuels and chemical feedstock. Apart from the high economic potentials, UCG may induce site‐specific environmental impacts, including ground surface subsidence and pollutant migration of UCG by-products into shallow freshwater aquifers. Sustainable and efficient UCG operation requires a thorough understanding of the coupled thermal, hydraulic and mechanical processes, occurring in the UCG reactor vicinity. The development and infrastructure costs of UCG trials are very high; therefore, numerical simulations of coupled processes in UCG are essential for the assessment of potential environmental impacts. Therefore, the aim of the present study is to assess UCG-induced permeability changes, potential hydraulic short circuit formation and non-isothermal multiphase fluid flow dynamics by means of coupled numerical simulations. Simulation results on permeability changes in the UCG reactor vicinity demonstrate that temperature-dependent thermo-mechanical parameters have to be considered in near-field assessments, only. Hence, far-field simulations do not become inaccurate, but benefit from increased computational efficiency when thermo-mechanical parameters are maintained constant. Simulations on potential hydraulic short circuit formation between single UCG reactors at regional-scale emphasize that geologic faults may induce hydraulic connections, and thus compromise efficient UCG operation. In this context, the steam jacket surrounding high-temperature UCG reactors plays a vital role in avoiding UCG by-products escaping into freshwater aquifers and in minimizing energy consumption by formation fluid evaporation. A steam jacket emerges in the close reactor vicinity due to phase transition of formation water and is a non-isothermal flow phenomenon. Considering this complex multiphase flow behavior, an innovative conceptual modeling approach, validated against field data, enables the quantification and prediction of UCG reactor water balances. The findings of this doctoral thesis provide an important basis for integration of thermo-hydro-mechanical simulations in UCG, required for the assessment and mitigation of its potential environmental impacts as well as optimization of its efficiency.
Contemporary multi-core processors are parallel systems that also provide shared memory for programs running on them. Both the increasing number of cores in so-called many-core systems and the still growing computational power of the cores demand for memory systems that are able to deliver high bandwidths. Caches are essential components to satisfy this requirement. Nevertheless, hardware-based cache coherence in many-core chips faces practical limits to provide both coherence and high memory bandwidths. In addition, a shift away from global coherence can be observed. As a result, alternative architectures and suitable programming models need to be investigated.
This thesis focuses on fast communication for non-cache-coherent many-core architectures. Experiments are conducted on the Single-Chip Cloud Computer (SCC), a non-cache-coherent many-core processor with 48 mesh-connected cores. Although originally designed for message passing, the results of this thesis show that shared memory can be efficiently used for one-sided communication on this kind of architecture. One-sided communication enables data exchanges between processes where the receiver is not required to know the details of the performed communication. In the notion of the Message Passing Interface (MPI) standard, this type of communication allows to access memory of remote processes. In order to support this communication scheme on non-cache-coherent architectures, both an efficient process synchronization and a communication scheme with software-managed cache coherence are designed and investigated.
The process synchronization realizes the concept of the general active target synchronization scheme from the MPI standard. An existing classification of implementation approaches is extended and used to identify an appropriate class for the non-cache-coherent shared memory platform. Based on this classification, existing implementations are surveyed in order to find beneficial concepts, which are then used to design a lightweight synchronization protocol for the SCC that uses shared memory and uncached memory accesses. The proposed scheme is not prone to process skew and also enables direct communication as soon as both communication partners are ready. Experimental results show very good scaling properties and up to five times lower synchronization latency compared to a tuned message-based MPI implementation for the SCC.
For the communication, SCOSCo, a shared memory approach with software-managed cache coherence, is presented. According requirements for the coherence that fulfill MPI's separate memory model are formulated, and a lightweight implementation exploiting SCC hard- and software features is developed. Despite a discovered malfunction in the SCC's memory subsystem, the experimental evaluation of the design reveals up to five times better bandwidths and nearly four times lower latencies in micro-benchmarks compared to the SCC-tuned but message-based MPI library. For application benchmarks, like a parallel 3D fast Fourier transform, the runtime share of communication can be reduced by a factor of up to five. In addition, this thesis postulates beneficial hardware concepts that would support software-managed coherence for one-sided communication on future non-cache-coherent architectures where coherence might be only available in local subdomains but not on a global processor level.
In der vorliegenden Dissertation werden lebensweltliche Erfahrungszusammenhänge in 128 Aufsätzen ausländischer Studierender, die oft auch als Bildungsausländer bezeichnet werden, und grundsätzliche Prozesse bei der Herausbildung sowie Veränderung kollektiver Zuschreibungen im Rahmen der sozialen Identitätsbildung hermeneutisch untersucht.
Mit Hilfe der nach der empirischen Methode der Grounded Theory kodierten Interpretationsergebnisse werden in der qualitativen Längsschnittstudie Vergleiche angestellt, sowohl fallintern als auch fallübergreifend, um Muster zu entdecken, Typologien zu konstruieren und die jeweiligen (kulturellen) Horizonte in den Aufsätzen zu verallgemeinern.
Neben der Grounded Theory bildet die Theorie der „alltäglichen Lebenswelt“ (Alfred Schütz) eine Basis der Herangehensweise an die Untersuchung der Aufsätze. In diesem Kontext wird ausgehend von der graduellen Unterteilung der Fremdheit in alltägliche, strukturelle und radikale Fremdheit sowie ausgehend von Goffmans Identitätskonzept der Frage nachgegangen, inwieweit sich in den untersuchten Texten die Bildung und Veränderung sozialer Identitäten feststellen lassen. Dabei werden Akkulturationsprozesse und Prozesse der Selbstidentifikation, bezüglich einer angenommenen Gemeinschaft, analysiert, die von kollektiven (kulturellen) Schemata bestimmt sind. In diesem Zusammenhang kann die vorliegende Dissertation zeigen, dass sich bestimmte kulturelle Schemata in der Auseinandersetzung mit dem vormals neuen Leben in Deutschland herausgebildet haben und bestimmte ältere Erfahrungen immer wieder zur Bestätigung dieser Bilder bzw. Erfahrungsschemata herangezogen und wie der Abdruck in Gestein fossiliert werden.
This study was inspired by the desire to contribute to literature on performance management from the context of a developing country. The guiding research questions were: How do managers use performance information in decision making? Why do managers use performance information the way they do? The study was based on theoretical strands of neo-patrimonialism and new institutionalism. The nature of the inquiry informed the choice of a qualitative case study research design. Data was assembled through face-to-face interviews, some observations, and collection of documents from managers at the levels of the directorate, division, and section/units. The managers who were the focus of this study are current or former staff members of the state departments in Kenya’s national Ministry of Agriculture, Livestock, and Fisheries as well as from departments responsible for coordination of performance related reforms.
The findings of this study show that performance information is regularly produced but its use by managers varies. Examples of use include preparing reports to external bodies, making decisions for resource re-allocation, making recommendations for rewards and sanctions, and policy advisory. On categorizing the forms of use as passive, purposeful, political or perverse, evidence shows that they overlap and that some of the forms are so closely related that it is difficult to separate them empirically.
On what can explain the forms of use established, four factors namely; political will and leadership; organizational capacity; administrative culture; and managers’ interests and attitudes, were investigated. While acknowledging the interrelatedness and even overlapping of the factors, the study demonstrates that there is explanatory power to each though with varying depth and scope. The study thus concludes that: Inconsistent political will and leadership for performance management reforms explain forms of use that are passive, political and perverse. Low organizational capacity could best explain passive and some limited aspects of purposeful use. Informal, personal and competitive administrative culture is associated with purposeful use and mostly with political and perverse use. Limited interest and apprehensive attitude are best associated with passive use.
The study contributes to the literature particularly in how institutions in a context of neo-patrimonialism shape performance information use. It recommends that further research is necessary to establish how neo-patrimonialism positively affects performance oriented reforms. This is interesting in particular given the emerging thinking on pockets of effectiveness and developmental patrimonialism. This is important since it is expected that performance related reforms will continue to be advocated in developing countries in the foreseeable future.
Im Rahmen dieser Arbeit wurden zum einen erste Oligospiro(thio)ketal (OS(T)K)-basierte Modellsysteme (molekulare Sonden) für abstandsabhängige Messungen mittels Förster-Resonanz-Energietransfer (FRET) und zum anderen Sensorfluorophore, basierend auf einem DBD-Fluorophor und BAPTA, zur Messung der intrazellulären Calcium-Konzentration dargestellt.
Für die Synthese von molekularen Sonden für abstandsabhängige Messungen wurden verschiedenste einfach- und doppelt-markierte OS(T)K-Stäbe entwickelt und spektroskopisch untersucht. Die OS(T)K-Stäbe, sogenannte molekulare Stäbe, dienten als starre Abstandshalter zwischen den Fluorophoren. Als Fluorophore wurden Derivate von 6,7-Dihydroxy-4-methylcoumarin (Donor) und Acyl-DBD (Akzeptor) verwendet, die zusammen ein FRET-Paar bilden. Die Fluorophore wurden so funktionalisiert, dass sie sowohl unbeweglich bzw. „starr“, als auch beweglich bzw. „flexibel“ an den OS(T)K-Stab gebunden werden konnten. Für die Synthese der OS(T)K-Stäbe wurden ebenfalls eine Reihe an unterschiedlich langen und kurzen Stabbausteinen synthetisiert. Auf diese Weise wurden eine Vielzahl an verschiedensten einfach- und doppelt-markierten OS(T)K-Stäben dargestellt, deren Fluorophore sowohl „starr“ als auch „flexibel“ gebunden sind. Die dargestellten Stäbe wurden in verschiedensten Lösungsmitteln spektroskopisch untersucht, um anschließend das Verhalten in Vesikel, die eine biomimetische Umgebung darstellen, zu beurteilen. Es wurde festgestellt, dass sich die Stäbe erfolgreich in die Vesikelmembran einlagerten und hohe FRET-Effizienzen aufweisen.
Des Weiteren wurde ein FRET-Paar dargestellt, das sich durch 2-Photonenabsorpion im NIR-Bereich anregen lässt. Es wurde in den lebenden Zellen mittels Fluoreszenzlebenszeitmikroskopie (FLIM) untersucht.
Zur Untersuchung von intrazellulärem Calcium wurden zwei verschiedene DBD-Fluorophore über einen kurzen Linker mit dem Calcium-Chelator BAPTA verknüpft. Die dargestellten Fluorophore wurden sowohl in vitro als auch in vivo auf ihre Calcium-Sensitivität überprüft. Mittels FLIM wurden in lebenden Zellen die Fluoreszenzlebenszeitverteilungen der Fluorophore nach Calcium-Konzentrationsänderungen detektiert.
Proteins are molecules that are essential for life and carry out an enormous number of functions in organisms. To this end, they change their conformation and bind to other molecules. However, the interplay between conformational change and binding is not fully understood. In this work, this interplay is investigated with molecular dynamics (MD) simulations of the protein-peptide system Mdm2-PMI and by analysis of data from relaxation experiments.
The central task it to uncover the binding mechanism, which is described by the sequence of (partial) binding events and conformational change events including their probabilities. In the simplest case, the binding mechanism is described by a two-step model: binding followed by conformational change or conformational change followed by binding. In the general case, longer sequences with multiple conformational changes and partial binding events are possible as well as parallel pathways that differ in their sequences of events. The theory of Markov state models (MSMs) provides the theoretical framework in which all these cases can be modeled. For this purpose, MSMs are estimated in this work from MD data, and rate equation models, which are related to MSMs, are inferred from experimental relaxation data.
The MD simulation and Markov modeling of the PMI-Mdm2 system shows that PMI and Mdm2 can bind via multiple pathways. A main result of this work is a dissociation rate on the order of one event per second, which was calculated using Markov modeling and is in agreement with experiment. So far, dissociation rates and transition rates of this magnitude have only been calculated with methods that speed up transitions by acting with time-dependent, external forces on the binding partners. The simulation technique developed in this work, in contrast, allows the estimation of dissociation rates from the combination of free energy calculation and direct MD simulation of the fast binding process. Two new statistical estimators TRAM and TRAMMBAR are developed to estimate a MSM from the joint data of both simulation types.
In addition, a new analysis technique for time-series data from chemical relaxation experiments is developed in this work. It allows to identify one of the above-mentioned two-step mechanisms as the mechanism that underlays the data. The new method is valid for a broader range of concentrations than previous methods and therefore allows to choose the concentrations such that the mechanism can be uniquely identified. It is successfully tested with data for the binding of recoverin to a rhodopsin kinase peptide.
Einleitung: Die Erdnussallergie zählt zu den häufigsten Nahrungsmittelallergien im Kindesalter. Bereits kleine Mengen Erdnuss (EN) können zu schweren allergischen Reaktionen führen. EN ist der häufigste Auslöser einer lebensbedrohlichen Anaphylaxie bei Kindern und Jugendlichen. Im Gegensatz zu anderen frühkindlichen Nahrungsmittelallergien entwickeln Patienten mit einer EN-Allergie nur selten eine natürliche Toleranz. Seit mehreren Jahren wird daher an kausalen Therapiemöglichkeiten für EN-Allergiker, insbesondere an der oralen Immuntherapie (OIT), geforscht. Erste kleinere Studien zur OIT bei EN-Allergie zeigten erfolgsversprechende Ergebnisse. Im Rahmen einer randomisierten, doppelblind, Placebo-kontrollierten Studie mit größerer Fallzahl werden in der vorliegenden Arbeit die klinische Wirksamkeit und Sicherheit dieser Therapieoption bei Kindern mit EN-Allergie genauer evaluiert. Des Weiteren werden immunologische Veränderungen sowie die Lebensqualität und Therapiebelastung unter OIT untersucht.
Methoden: Kinder zwischen 3-18 Jahren mit einer IgE-vermittelten EN-Allergie wurden in die Studie eingeschlossen. Vor Beginn der OIT wurde eine orale Provokation mit EN durchgeführt. Die Patienten wurden 1:1 randomisiert und entsprechend der Verum- oder Placebogruppe zugeordnet. Begonnen wurde mit 2-120 mg EN bzw. Placebo pro Tag, abhängig von der Reaktionsdosis bei der oralen Provokation. Zunächst wurde die tägliche OIT-Dosis alle zwei Wochen über etwa 14 Monate langsam bis zu einer Erhaltungsdosis von mindestens 500 mg EN (= 125 mg EN-Protein, ~ 1 kleine EN) bzw. Placebo gesteigert. Die maximal erreichte Dosis wurde dann über zwei Monate täglich zu Hause verabreicht. Im Anschluss erfolgte erneut eine orale Provokation mit EN. Der primäre Endpunkt der Studie war die Anzahl an Patienten der Verum- und Placebogruppe, die unter oraler Provokation nach OIT ≥1200 mg EN vertrugen (=„partielle Desensibilisierung“). Sowohl vor als auch nach OIT wurde ein Hautpricktest mit EN durchgeführt und EN-spezifisches IgE und IgG4 im Serum bestimmt. Außerdem wurden die Basophilenaktivierung sowie die Ausschüttung von T-Zell-spezifischen Zytokinen nach Stimulation mit EN in vitro gemessen. Anhand von Fragebögen wurde die Lebensqualität vor und nach OIT sowie die Therapiebelastung während OIT erfasst.
Ergebnisse: 62 Patienten wurden in die Studie eingeschlossen und randomisiert. Nach etwa 16 Monaten unter OIT zeigten 74,2% (23/31) der Patienten der Verumgruppe und nur 16,1% (5/31) der Placebogruppe eine „partielle Desensibilisierung“ gegenüber EN (p<0,001). Im Median vertrugen Patienten der Verumgruppe 4000 mg EN (~8 kleine EN) unter der Provokation nach OIT wohingegen Patienten der Placebogruppe nur 80 mg EN (~1/6 kleine EN) vertrugen (p<0,001). Fast die Hälfte der Patienten der Verumgruppe (41,9%) tolerierten die Höchstdosis von 18 g EN unter Provokation („komplette Desensibilisierung“). Es zeigte sich ein vergleichbares Sicherheitsprofil unter Verum- und Placebo-OIT in Bezug auf objektive Nebenwirkungen. Unter Verum-OIT kam es jedoch signifikant häufiger zu subjektiven Nebenwirkungen wie oralem Juckreiz oder Bauchschmerzen im Vergleich zu Placebo (3,7% der Verum-OIT-Gaben vs. 0,5% der Placebo-OIT-Gaben, p<0,001). Drei Kinder der Verumgruppe (9,7%) und sieben Kinder der Placebogruppe (22,6%) beendeten die Studie vorzeitig, je zwei Patienten beider Gruppen aufgrund von Nebenwirkungen. Im Gegensatz zu Placebo, zeigten sich unter Verum-OIT signifikante immunologische Veränderungen. So kam es zu einer Abnahme des EN-spezifischen Quaddeldurchmessers im Hautpricktest, einem Anstieg der EN-spezifischen IgG4-Werte im Serum sowie zu einer verminderten EN-spezifischen Zytokinsekretion, insbesondere der Th2-spezifischen Zytokine IL-4 und IL-5. Hinsichtlich der EN-spezifischen IgE-Werte sowie der EN-spezifischen Basophilenaktivierung zeigten sich hingegen keine Veränderungen unter OIT. Die Lebensqualität von Kindern der Verumgruppe war nach OIT signifikant verbessert, jedoch nicht bei Kindern der Placebogruppe. Während der OIT wurde die Therapie von fast allen Kindern (82%) und Müttern (82%) als positiv bewertet (= niedrige Therapiebelastung).
Diskussion: Die EN-OIT führte bei einem Großteil der EN-allergischen Kinder zu einer Desensibilisierung und einer deutlich erhöhten Reaktionsschwelle auf EN. Somit sind die Kinder im Alltag vor akzidentellen Reaktionen auf EN geschützt, was die Lebensqualität der Kinder deutlich verbessert. Unter den kontrollierten Studienbedingungen zeigte sich ein akzeptables Sicherheitsprofil, mit vorrangig milder Symptomatik. Die klinische Desensibilisierung ging mit Veränderungen auf immunologischer Ebene einher. Langzeitstudien zur EN-OIT müssen jedoch abgewartet werden, um die klinische und immunologische Wirksamkeit hinsichtlich einer möglichen langfristigen oralen Toleranzinduktion sowie die Sicherheit unter langfristiger OIT zu untersuchen, bevor das Therapiekonzept in die Praxis übertragen werden kann.
Approaching physical limits in speed and size of today's magnetic storage and processing technologies demands new concepts for controlling magnetization and moves researches on optically induced magnetic dynamics. Studies on photoinduced magnetization dynamics and their underlying mechanisms have been primarily performed on ferromagnetic metals. Ferromagnetic dynamics bases on transfer of the conserved angular momentum connected with atomic magnetic moments out of the parallel aligned magnetic system into other degrees of freedom.
In this thesis the so far rarely studied response of antiferromagnetic order to ultra-short optical laser pulses in a metal is investigated. The experiments were performed at the FemtoSpex slicing facility at the storage ring BESSY II, an unique source for ultra-short elliptically polarized x-ray pulses. Laser-induced changes of the 4f-magnetic order parameter in ferro- and antiferromagnetic dysprosium (Dy), were studied by x-ray methods, which yield directly comparable quantities. The discovered fundamental differences in the temporal and spatial behavior of ferro- and antiferrmagnetic dynamics are assinged to an additional channel for angular momentum transfer, which reduces the antiferromagnetic order by redistributing angular momentum within the non-parallel aligned magnetic system, and hence conserves the zero net magnetization. It is shown that antiferromagnetic dynamics proceeds considerably faster and more energy-efficient than demagnetization in ferromagnets. By probing antiferromagnetic order in time and space, it is found to be affected along the whole sample depth of an in situ grown 73 nm tick Dy film. Interatomic transfer of angular momentum via fast diffusion of laser-excited 5d electrons is held responsible for the out-most long-ranging effect. Ultrafast ferromagnetic dynamics can be expected to base on the same origin, which however leads to demagnetization only in regions close to interfaces caused by super-diffusive spin transport. Dynamics due to local scattering processes of excited but less mobile electrons, occur in both magnetic alignments only in directly excited regions of the sample and on slower pisosecond timescales. The thesis provides fundamental insights into photoinduced magnetic dynamics by directly comparing ferro- and antiferromagnetic dynamics in the same material and by consideration of the laser-induced magnetic depth profile.
The goal of this thesis is related to the question how to introduce and combine simultaneously plasmonic and photoswitching properties to different nano-objects. In this thesis I investigate the complexes between noble metal nanoparticles and cationic surfactants containing azobenzene units in their hydrophobic tail, employing absorption spectroscopy, surface zeta-potential, and electron microscopy.
In the first part of the thesis, the formation of complexes between negatively charged laser ablated spherical gold nanoparticles and cationic azobenzene surfactants in trans- conformation is explored. It is shown that the constitution of the complexes strongly depends on a surfactant-to-gold molar ratio. At certain molar ratios, particle self-assembly into nanochains and their aggregation have been registered. At higher surfactant concentrations, the surface charge of nanoparticles turned positive, attributed to the formation of the stabilizing double layer of azobenzene surfactants on gold nanoparticle surfaces. These gold-surfactant complexes remained colloidally stable. UV light induced trans-cis isomerization of azobenzene surfactant molecules and thus perturbed the stabilizing surfactant shell, causing nanoparticle aggregation. The results obtained with silver and silicon nanoparticles mimick those for the comprehensively studied gold nanoparticles, corroborating the proposed model of complex formation.
In the second part, the interaction between plasmonic metal nanoparticles (Au, Ag, Pd, alloy Au-Ag, Au-Pd), as well as silicon nanoparticles, and cis-isomers of azobenzene containing compounds is addressed. Cis-trans thermal isomerization of azobenzenes was enhanced in the presence of gold, palladium, and alloy gold-palladium nanoparticles. The influence of the surfactant structure and nanoparticle material on the azobenzene isomerization rate is expounded. Gold nanoparticles showed superior catalytic activity for thermal cis-trans isomerization of azobenzenes. In a joint project with theoretical chemists, we demonstrated that the possible physical origin of this phenomenon is the electron transfer between azobenzene moieties and nanoparticle surfaces.
In the third part, complexes between gold nanorods and azobenzene surfactants with different tail length were exposed to UV and blue light, inducing trans-cis and cis-trans isomerization of surfactant, respectively. At the same time, the position of longitudinal plasmonic absorption maximum of gold nanorods experienced reversible shift responding to the changes in local dielectric environment. Surface plasmon resonance condition allowed the estimation of the refractive index of azobenzene containing surfactants in solution.
Carbohydrate-protein interactions are ubiquitous in nature. They provide the initial molecular contacts in many cell-cell processes as for example immune responses, signal transduction, egg fertilization and infection processes of pathogenic viruses and bacteria. Furthermore, bacteria themselves are infected by bacteriophages, viruses which can cause the bacterial lysis, but do not affect other hosts. The infection process of a bacteriophage involves the specific detection and binding of the bacterium, which can be based on a carbohydrate-protein interaction. The mechanism of specific detection of pathogenic bacteria can thereby be useful for the development of bacteria sensors in the food industry or for tools in diagnostics.
Bacteriophages of the Podoviridae family use tailspike proteins for the specific detection of enteritis causing bacteria as Escherichia coli, Salmonella spp. or Shigella flexneri. The tailspike protein provides the first contact by binding to the carbohydrate containing O-antigen part of lipopolysaccharide in the Gram-negative cell wall. After binding to O-antigen repeating units, the enzymatic activity of tailspike proteins leads to cleavage of the carbohydrate chains, which enables the bacteriophage to approach the bacterial surface for DNA injection. Tailspike proteins thereby exhibit a relatively low affinity to the oligosaccharide structures of O-antigen due to the necessary binding, cleavage and release cycle, compared for example to antibodies. In this work it was aimed to study the determinants that influence carbohydrate affinity in the extended TSP binding grooves. This is a prerequisite to design a high-affinity tailspike protein based bacteria sensor.
For this purpose the tailspike protein of the bacteriophage Sf6 (Sf6 TSP) was used, which specifically binds Shigella flexneri Y O-antigen with two tetrasaccharide repeating units at the intersubunits of the trimeric β-helix protein. The Sf6 TSP endorhamnosidase cleaves the O-antigen, which leads to an octasaccharide as the main product. The binding affinity of inactive Sf6 TSP towards polysaccharide was characterized by fluorescence titration experiments and surface plasmon resonance (SPR).
Moreover, cysteine mutations were introduced into the Sf6 TSP binding site for the covalent thiol-coupling of an environment-sensitive fluorescent label to obtain a sensor for Shigella flexneri Y based on TSP-O-antigen recognition. This sensor showed a more than 100 % amplitude increase of a visible light fluorescence upon the binding of a polysaccharide test solution. Improvements of the TSP sensor can be achieved by increasing the tailspike affinity towards the O-antigen. Therefore molecular dynamics simulations evaluating ligand flexibility, hydrogen bond occupancies and water network distributions were used for affinity prediction on the available cysteine mutants of Sf6 TSP. The binding affinities were experimentally analyzed by SPR. This combined computational and experimental set-up for the design of a high-affinity carbohydrate binding protein could successfully distinguish strongly increased and decreased affinities of single amino acid mutants.
A thermodynamically and structurally well characterized set of another tailspike protein HK620 TSP with high-affinity mutants was used to evaluate the influence of water molecules on binding affinity. The free enthalpy of HK620 TSP oligosaccharide complex formation thereby either derived from the replacement of a conserved water molecule or by immobilization of two water molecules upon ligand binding. Furthermore, the enthalpic and entropic contributions of water molecules in a hydrophobic binding pocket could be assigned by free energy calculations. The findings in this work can be helpful for the improvement of carbohydrate docking and carbohydrate binding protein engineering algorithms in the future.
In this thesis, I develop a theoretical implementation of prosodic reconstruction and apply it to the empirical domain of German sentences in which part of a focus or contrastive topic is fronted.
Prosodic reconstruction refers to the idea that sentences involving syntactic movement show prosodic parallels with corresponding simpler structures without movement. I propose to model this recurrent observation by ordering syntax-prosody mapping before copy deletion.
In order to account for the partial fronting data, the idea is extended to the mapping between prosody and information structure. This assumption helps to explain why object-initial sentences containing a broad focus or broad contrastive topic show similar prosodic and interpretative restrictions as sentences with canonical word order.
The empirical adequacy of the model is tested against a set of gradient acceptability judgments.
Although it has become common practice to build applications based on the reuse of existing components or services, technical complexity and semantic challenges constitute barriers to ensuring a successful and wide reuse of components and services. In the geospatial application domain, the barriers are self-evident due to heterogeneous geographic data, a lack of interoperability and complex analysis processes.
Constructing workflows manually and discovering proper services and data that match user intents and preferences is difficult and time-consuming especially for users who are not trained in software development. Furthermore, considering the multi-objective nature of environmental modeling for the assessment of climate change impacts and the various types of geospatial data (e.g., formats, scales, and georeferencing systems) increases the complexity challenges.
Automatic service composition approaches that provide semantics-based assistance in the process of workflow design have proven to be a solution to overcome these challenges and have become a frequent demand especially by end users who are not IT experts. In this light, the major contributions of this thesis are:
(i) Simplification of service reuse and workflow design of applications for climate impact analysis by following the eXtreme Model-Driven Development (XMDD) paradigm.
(ii) Design of a semantic domain model for climate impact analysis applications that comprises specifically designed services, ontologies that provide domain-specific vocabulary for referring to types and services, and the input/output annotation of the services using the terms defined in the ontologies.
(iii) Application of a constraint-driven method for the automatic composition of workflows for analyzing the impacts of sea-level rise. The application scenario demonstrates the impact of domain modeling decisions on the results and the performance of the synthesis algorithm.
Für den Industrialisierungsprozess von Entwicklungs- und Schwellenländern haben ausländische Direktinvestitionen (ADI) eine wichtige Funktion. Sie können zum einen zu einer Erhöhung des industriellen Output des Ziellandes führen und zum anderen als Träger von technologischem Wissen fungieren. Neues Wissen kann den Empfängerländern der ADI durch Spillovereffekte und Technologietransfers ausländischer Tochterunternehmen zufließen. Diese Arbeit soll Antworten auf die Fragen geben, durch welche Mechanismen Spillovereffekte und Technologietransfers ausgelöst werden und wie Entwicklungs- und Schwellenländern diesen Wissenszufluss zur Beschleunigung ihres Industrialisierungsprozesses einsetzen können. Hierfür wird ein Konzept zur Förderung von Spillovereffekten entwickelt. Weiterhin wird ein theoretisches Modell entwickelt, in dem der Technologietransfer ausländischer Exportplattformen erstmals in Abhängigkeit des Anteils der Vorprodukte, die im Gastland nachgefragt werden, untersucht. In den Fallstudien Irland und Malaysia werden die Ergebnisse des theoretischen Modells sowie des entwickelten Konzepts illustriert.
Im Sinne des Refinements von Tierversuchen sollen alle Bedingungen während der Zucht, der Haltung und des Transports von zu Versuchszwecken gehaltenen Tieren und alle Methoden während des Versuchs so verbessert werden, dass die verwendeten Tiere ein minimales Maß an potentiellem Distress, Schmerzen oder Leiden erfahren. Zudem soll ihr Wohlbefinden durch die Möglichkeit des Auslebens speziesspezifischer Verhaltensweisen und die Anwendung tierschonender Verfahren maximal gefördert werden. Zur Etablierung von Grundsätzen des Refinements sind grundlegende Kenntnisse über die physiologischen Bedürfnisse und Verhaltensansprüche der jeweiligen Spezies unabdingbar. Die Experimentatoren sollten das Normalverhalten der Tiere kennen, um potentielle Verhaltensabweichungen, wie Stereotypien, zu verstehen und interpretieren zu können. Standardisierte Haltungsbedingungen von zu Versuchszwecken gehaltenen Mäusen weichen in diversen Aspekten von der natürlichen Umgebung ab und erfordern eine gewisse Adaptation. Ist ein Tier über einen längeren Zeitraum unfähig, sich an die gegebenen Umstände anzupassen, können abnormale Verhaltensweisen, wie Stereotypien auftreten. Stereotypien werden definiert als Abweichungen vom Normalverhalten, die repetitiv und ohne Abweichungen im Ablauf ausgeführt werden, scheinbar keiner Funktion dienen und der konkreten Umweltsituation nicht immer entsprechen.
Bisher war unklar, in welchem Ausmaß stereotypes Verhalten den metabolischen Phänotyp eines Individuums beeinflusst. Ziel dieser Arbeit war es daher, das stereotype Verhalten der FVB/NJ-Maus erstmals detailliert zu charakterisieren, systematisch zusammenzutragen, welche metabolischen Konsequenzen dieses Verhalten bedingt und wie sich diese auf das Wohlbefinden der Tiere und die Verwendung stereotyper Tiere in Studien mit tierexperimentellem Schwerpunkt auswirken.
Der Versuch begann mit der Charakterisierung der mütterlichen Fürsorge in der Parentalgeneration. Insgesamt wurden 35 Jungtiere der F1-Generation vom Absatz an, über einen Zeitraum von 11 Wochen einzeln gehalten, kontinuierlich beobachtet, bis zum Versuchsende wöchentlich Kotproben gesammelt und das Körpergewicht bestimmt. Zusätzlich erfolgten begleitende Untersuchungen wie Verhaltenstests und die Erfassung der physischen Aktivität und metabolischer Parameter. Anschließend wurden u.a. die zerebralen Serotonin- und Dopamingehalte, fäkale Glucocorticoidlevels, hepatisches Glykogen und muskuläre Glykogen- und Triglyceridlevels bestimmt.
Nahezu unabhängig von der mütterlichen Herkunft entwickelte sich bei mehr als der Hälfte der 35 Jungtiere in der F1-Generation stereotypes Verhalten. Diese Daten deuten darauf hin, dass es keine Anzeichen für das Erlernen oder eine direkte genetische Transmission stereotypen Verhaltens bei der FVB/NJ-Maus gibt. Über den gesamten Beobachtungszeitraum zeichneten sich die stereotypen FVB/NJ-Mäuse durch ein eingeschränktes Verhaltensrepertoire aus. Zu Gunsten der erhöhten Aktivität und des Ausübens stereotypen Verhaltens lebten sie insgesamt weniger andere Verhaltensweisen (Klettern, Graben, Nagen) aus. Darüber hinaus waren Stereotypien sowohl im 24-Stunden Open Field Test als auch in der Messeinrichtung der indirekten Tierkalorimetrie mit einer erhöhten Aktivität und Motilität assoziiert, während die circadiane Rhythmik nicht divergierte. Diese erhöhte körperliche Betätigung spiegelte sich in den niedrigeren Körpergewichtsentwicklungen der stereotypen Tiere wieder. Außerdem unterschieden sich die Körperfett- und Körpermuskelanteile.
Zusammenfassend lässt sich sagen, dass das Ausüben stereotypen Verhaltens zu Differenzen im metabolischen Phänotyp nicht-stereotyper und stereotyper FVB/NJ-Mäuse führt. Im Sinne der „Guten Wissenschaftlichen Praxis“ sollte das zentrale Ziel jedes Wissenschaftlers sein, aussagekräftige und reproduzierbare Daten hervorzubringen. Jedoch können keine validen Resultate von Tieren erzeugt werden, die in Aspekten variieren, die für den vorgesehenen Zweck der Studie nicht berücksichtigt wurden. Deshalb sollten nicht-stereotype und stereotype Individuen nicht innerhalb einer Versuchsgruppe randomisiert werden. Stereotype Tiere demzufolge von geplanten Studien auszuschließen, würde allerdings dem Gebot des zweiten R’s – der Reduction – widersprechen. Um Refinement zu garantieren, sollte der Fokus auf der maximal erreichbaren Prävention stereotypen Verhaltens liegen. Diverse Studien haben bereits gezeigt, dass die Anreicherung der Haltungsumwelt (environmental enrichment) zu einer Senkung der Prävalenz von Stereotypien bei Mäusen führt, dennoch kommen sie weiterhin vor. Daher sollte environmental enrichment zukünftig weniger ein „Kann“, sondern ein „Muss“ sein – oder vielmehr: der Goldstandard. Zudem würde eine profunde phänotypische Charakterisierung dazu beitragen, Mausstämme zu erkennen, die zu Stereotypien neigen und den für den spezifischen Zweck am besten geeigneten Mausstamm zu identifizieren, bevor ein Experiment geplant wird.
Natural and potentially hazardous events occur on the Earth’s surface every day. The most destructive of these processes must be monitored, because they may cause loss of lives, infrastructure, and natural resources, or have a negative effect on the environment. A variety of remote sensing technologies allow the recoding of data to detect these processes in the first place, partly based on the diagnostic landforms that they form. To perform this effectively, automatic methods are desirable.
Universal detection of natural hazards is challenging due to their differences in spatial impacts, timing and longevity of consequences, and the spatial resolution of remote-sensing data. Previous studies have reported that topographic metrics such as roughness, which can be captured from digital elevation data, can reveal landforms diagnostic of natural hazards, such as gullies, dunes, lava fields, landslides and snow avalanches, as these landforms tend to be more heterogeneous than the surrounding landscape. A single roughness metric is often limited in such detections; however, a more complex approach that exploits the spatial relation and the location of objects, such as object-based image analysis (OBIA), is desirable.
In this thesis, I propose a topographic roughness measure derived from an airborne laser scanning (ALS) digital terrain model (DTM) and discuss its performance in detecting landforms principally diagnostic of natural hazards. I further develop OBIA-based algorithms for the detection of snow avalanches using near-infrared (NIR) aerial images, and the size (changes) of mountain lakes using LANDSAT satellite images. I quantitatively test and document how the level of difficulty in detecting these very challenging landforms depends on the input data resolution, the derivatives that could be evaluated from images and DTMs, the size, shape and complexity of landforms, and the capabilities of obtaining the information in the data. I demonstrate that surface roughness is a promising metric for detecting different landforms in diverse environments, and that OBIA assists significantly in detecting parts of lakes and snow avalanches that may not be correctly assigned by applying only the thresholding of spectral properties of data and their derivatives.
The curvature-based surface roughness parameter allows the detection of gullies, dunes, lava fields and landslides with a user’s accuracy of 0.63, 0.21, 0.53, and 0.45, respectively. The OBIA algorithms for detecting lakes and snow avalanches obtained user’s accuracy of 0.98, and 0.78, respectively. Most of the analysed landforms constituted only a small part of the entire dataset, and therefore the user’s accuracy is the most appropriate performance measure that should be given in a such classification, because it tells how many automatically-extracted pixels in fact represent the object that one wants to classify, and its calculation does not take the second (background) class into account. One advantage of the proposed roughness parameter is that it allows the extraction of the heterogeneity of the surface without the need for data detrending. The OBIA approach is novel in that it allows the classification of lakes regardless of the physical state of their water, and also allows the separation of frozen lakes from glaciers that have very similar water indices used in purely optical remote sensing applications. The algorithm proposed for snow avalanches allows the detection of release zones, tracks, and deposition zones by verifying the snow heterogeneity based on a roughness metric evaluated from a water index, and by analysing the local relation of segments with their neighbouring objects. This algorithm contains few steps, which allows for the simultaneous classification of avalanches that occur on diverse mountain slopes and differ in size and shape.
This thesis contributes to natural hazard research as it provides automatic solutions to tracking six different landforms that are diagnostic of natural hazards over large regions. This is a step toward delineating areas susceptible to the processes producing these landforms and the improvement of hazard maps.
This project was focused on generating ultra thin stimuli responsive membranes with an embedded transmembrane protein to act as the pore. The membranes were formed by crosslinking of transmembrane protein polymer conjugates. The conjugates were self assembled on air water interface and the polymer chains crosslinked using a UV crosslinkable comonomer to engender the membrane. The protein used for the studies reported herein was one of the largest transmembrane channel proteins, ferric hydroxamate uptake protein component A (FhuA), found in the outer membrane of Escherichia coli (E. coli). The wild type protein and three genetic variants of FhuA were provided by the group of Prof. Schwaneberg in Aachen. The well known thermo responsive poly(N isopropylacrylamide) (PNIPAAm) and the pH and thermo responsive polymer poly((2-dimethylamino)ethyl methacrylate) (PDMAEMA) were conjugated to FhuA and the genetic variants via controlled radical polymerization (CRP) using grafting from technique. These polymers were chosen because they would provide stimuli handles in the resulting membranes. The reported polymerization was the first ever attempt to attach polymer chains onto a membrane protein using site specific modification.
The conjugate synthesis was carried out in two steps – a) FhuA was first converted into a macroinitiator by covalently linking a water soluble functional CRP initiator to the lysine residues. b) Copper mediated CRP was then carried out in pure buffer conditions with and without sacrificial initiator to generate the conjugates.
The challenge was carrying out the modifications on FhuA without denaturing it. FhuA, being a transmembrane protein, requires amphiphilic species to stabilize its highly hydrophobic transmembrane region. For the experiments reported in this thesis, the stabilizing agent was 2 methyl 2,4-pentanediol (MPD). Since the buffer containing MPD cannot be considered a purely aqueous system, and also because MPD might interfere with the polymerization procedure, the reaction conditions were first optimized using a model globular protein, bovine serum albumin (BSA). The optimum conditions were then used for the generation of conjugates with FhuA.
The generated conjugates were shown to be highly interfacially active and this property was exploited to let them self assemble onto polar apolar interfaces. The emulsions stabilized by particles or conjugates are referred to as Pickering emulsions. Crosslinking conjugates with a UV crosslinkable co monomer afforded nano thin micro compartments. Interfacial self assembly at the air water interface and subsequent UV crosslinking also yielded nano thin, stimuli responsive membranes which were shown to be mechanically robust. Initial characterization of the flux and permeation of water through these membranes is also reported herein. The generated nano thin membranes with PNIPAAm showed reduced permeation at elevated temperatures owing to the resistance by the hydrophobic and thus water-impermeable polymer matrix, hence confirming the stimulus responsivity.
Additionally, as a part of collaborative work with Dr. Changzhu Wu, TU Dresden, conjugates of three enzymes with current/potential industrial relevance (candida antarctica lipase B, benzaldehyde lyase and glucose oxidase) with stimuli responsive polymers were synthesized. This work aims at carrying out cascade reactions in the Pickering emulsions generated by self assembled enzyme polymer conjugate.
Understanding the distribution of species is fundamental for biodiversity conservation, ecosystem management, and increasingly also for climate impact assessment. The presence of a species in a given site depends on physiological limitations (abiotic factors), interactions with other species (biotic factors), migratory or dispersal processes (site accessibility) as well as the continuing
effects of past events, e.g. disturbances (site legacy). Existing approaches to predict species distributions either (i) correlate observed species occurrences with environmental variables describing abiotic limitations, thus ignoring biotic interactions, dispersal and legacy effects (statistical species distribution model, SDM); or (ii) mechanistically model the variety of processes determining species distributions (process-based model, PBM). SDMs are widely used due to their easy applicability and ability to handle varied data qualities. But they fail to reproduce the dynamic response of species distributions to changing conditions. PBMs are expected to be superior in this respect, but they need very specific data unavailable for many species, and are often more complex and require more computational effort. More recently, hybrid models link the two approaches to combine their respective strengths.
In this thesis, I apply and compare statistical and process-based approaches to predict species distributions, and I discuss their respective limitations, specifically for applications in changing environments. Detailed analyses of SDMs for boreal tree species in Finland reveal that nonclimatic predictors - edaphic properties and biotic interactions - are important limitations at the treeline, contesting the assumption of unrestricted, climatically induced range expansion. While the estimated SDMs are successful within their training data range, spatial and temporal model transfer fails. Mapping and comparing sampled predictor space among data subsets identifies spurious extrapolation as the plausible explanation for limited model transferability. Using these findings, I analyze the limited success of an established PBM (LPJ-GUESS) applied to the same problem. Examination of process representation and parameterization in the PBM identifies implemented processes to adjust (competition between species, disturbance) and missing processes that are crucial in boreal forests (nutrient limitation, forest management). Based on climatic correlations shifting over time, I stress the restricted temporal transferability of bioclimatic limits used in LPJ-GUESS and similar PBMs. By critically assessing the performance of SDM and PBM in this application, I demonstrate the importance of understanding the limitations of the
applied methods.
As a potential solution, I add a novel approach to the repertoire of existing hybrid models. By simulation experiments with an individual-based PBM which reproduces community dynamics resulting from biotic factors, dispersal and legacy effects, I assess the resilience of coastal vegetation to abrupt hydrological changes. According to the results of the resilience analysis, I then modify temporal SDM predictions, thereby transferring relevant process detail from PBM to
SDM. The direction of knowledge transfer from PBM to SDM avoids disadvantages of current hybrid models and increases the applicability of the resulting model in long-term, large-scale applications. A further advantage of the proposed framework is its flexibility, as it is readily extended to other model types, disturbance definitions and response characteristics.
Concluding, I argue that we already have a diverse range of promising modelling tools at hand, which can be refined further. But most importantly, they need to be applied more thoughtfully. Bearing their limitations in mind, combining their strengths and openly reporting underlying assumptions and uncertainties is the way forward.
Mundos comunes
(2017)
A partir de la constatación de una serie de movimientos y diálogos artísticos, correspondientes a las décadas del setenta y ochenta, su tesis doctoral interroga la noción de “lo latinoamericano” en el ámbito del arte y la cultura. La investigación realiza un “viaje recopilatorio” de documentos a través de distintas ciudades europeas que permiten problematizar el lugar, la comunidad y la memoria cultural de lo latinoamericano.
Der technologische Wandel stellt Organisationen vor die Herausforderung, Innovationen möglichst schnell produktiv zu nutzen und damit einen Wettbewerbsvorteil zu erzielen. Der Erfolg der Technologieeinführung hängt stark mit der Schaffung von Akzeptanz bei den Mitarbeitern zusammen. Bestehende Ansätze wie die Diffusionstheorie (Rogers, 2003) oder das Technology Acceptance Model (Davis, 1989; Venkatesh und Davis, 1996; Venkatesh und Davis, 2000; Venkatesh, Morris u. a., 2003) widmen sich dem Organisationskontext jedoch nur am Rande. Ihre Modelle zielen auf die Übernahme einer Technologie in freier Entscheidung und im Marktkontext ab. Weiterhin beleuchten sie den Widerstand gegen Neuerungen nicht, welcher sich bei der verpflichtenden Übernahme bilden kann. Zur Untersuchung der Technologieeinführung und von Akzeptanzbildungsprozessen in Organisationen sind sie daher nur begrenzt nutzbar.
Das Ziel dieser Arbeit ist es daher, den spezifischen Einfluss des Kontextes Organisation auf die Akzeptanz und das Nutzungsverhalten herauszuarbeiten. Konkreter soll die Forschungsfrage geklärt werden, welchen Einfluss unterschiedliche Organisationstypen auf die Akzeptanz- und Nutzungsdynamik innerhalb von Organisationen haben. Hierfür wird die Erweiterung und Synthese bestehender Modelle der Akzeptanzforschung um organisationsspezifische Attribute vorgenommen. Das resultierende Modell erfasst die dynamische Entwicklung innerhalb der Organisation und ermöglicht damit die Beobachtung des Wandels. Die Funktionsweise des entwickelten Modells soll in einem Simulationsexperiment demonstriert und die Wirkung unterschiedlicher Organisationsformen verdeutlicht werden.
Das Modell vereint daher zwei Perspektiven: Die personale Perspektive fasst Akzeptanz als kognitiv-psychischen Prozess auf individueller Ebene. Dieser basiert auf den Kalkülen und Entscheidungen einzelner Personen. Zentral sind hierfür die Beiträge der Diffusionstheorie (Rogers, 2003) sowie das Technology Acceptance Model in seinen diversen Weiterentwicklungen und Veränderungen (Davis, 1989; Venkatesh und Davis, 1996; Venkatesh und Davis, 2000; Venkatesh, Morris u. a., 2003). Individuelle Faktoren aus unterschiedlichen Fit-Theorien (Goodhue und Thompson, 1995; Floyd, 1986; Liu, Lee und Chen, 2011; Parkes, 2013) werden genutzt, um diese Modelle anzureichern. Neben der Entwicklung
einer positiven, förderlichen Einstellung muss jedoch auch die Ablehnung und das offene Opponieren gegen die Innovation berücksichtigt werden (Patsiotis, Hughes und Webber, 2012).
Die organisatorische Perspektive hingegen sieht Akzeptanzentscheidungen eingebettet in den sozialen Kontext der Organisation. Die gegenseitige Beeinflussung basiert auf der Beobachtung der Umgebung und der Internalisierung sozialen Drucks. Dem steht in Organisationen die intendierte Beeinflussung in Form von Steuerung gegenüber. Beide Vorgänge formen das Akzeptanz- oder das Nutzungsverhalten der Mitarbeiter. Ausgehend von einem systemtheoretischen Organisationsbegriff werden unterschiedliche Steuerungsmedien (Luhmann, 1997; Fischer, 2009) vorgestellt. Diese können durch Steuerungsakteure
(Change Agents, Management) intendiert eingesetzt werden, um den Akzeptanz- und Nutzungsprozess über Interventionen zu gestalten.
Die Wirkung der Medien unterscheidet sich in verschiedenen Organisationstypen. Zur Analyse unterschiedlicher Organisationstypen werden die Konfigurationen nach Mintzberg (1979) herangezogen. Diese zeichnen sich durch unterschiedliche Koordinationsmechanismen aus, welche wiederum auf dem Einsatz von Steuerungsmedien beruhen.
Die Demonstration der Funktionsweise und Analysemöglichkeiten des entwickelten Modells erfolgt anhand eines Simulationsexperiments mittels der Simulationsplattform AnyLogic. Das Gültigkeitsspektrum wird anhand einer Sensitivitätsanalyse geprüft.
In der Simulation lassen sich spezifische Muster der Nutzung und Akzeptanzentwicklung nachweisen. Die Akzeptanz ist durch ein initiales Absinken und ein anschließendes gedämpftes Wachstum gekennzeichnet. Die Nutzung wird in der Organisation hingegen schnell durchgesetzt und verharrt dann auf einem stabilen Niveau. Für die Organisationstypen konnten unterschiedliche Effekte beobachtet werden. So eignet sich die bürokratische Steuerungsform zur Nutzungserhöhung, schafft es jedoch nicht, die Akzeptanz zu steigern. Organisationen, welche eher auf gegenseitige Abstimmung zur Koordination ausgelegt sind, erhöhen die Akzeptanz, jedoch nicht die Nutzung. Weiterhin ist die Entwicklung der Akzeptanz in diesem Organisationstyp sehr unsicher und weist einen hohen Schwankungsbereich auf.
Detection and Kirchhoff-type migration of seismic events by use of a new characteristic function
(2017)
The classical method of seismic event localization is based on the picking of body wave arrivals, ray tracing and inversion of travel time data. Travel time picks with small uncertainties are required to produce reliable and accurate results with this kind of source localization. Hence recordings, with a low Signal-to-Noise Ratio (SNR) cannot be used in a travel time based inversion. Low SNR can be related with weak signals from distant and/or low magnitude sources as well as with a high level of ambient noise. Diffraction stacking is considered as an alternative seismic event localization method that enables also the processing of low SNR recordings by mean of stacking the amplitudes of seismograms along a travel time function. The location of seismic event and its origin time are determined based on the highest stacked amplitudes (coherency) of the image function. The method promotes an automatic processing since it does not need travel time picks as input data.
However, applying diffraction stacking may require longer computation times if only limited computer resources are used. Furthermore, a simple diffraction stacking of recorded amplitudes could possibly fail to locate the seismic sources if the focal mechanism leads to complex radiation patterns which typically holds for both natural and induced seismicity.
In my PhD project, I have developed a new work flow for the localization of seismic events which is based on a diffraction stacking approach. A parallelized code was implemented for the calculation of travel time tables and for the determination of an image function to reduce computation time. In order to address the effects from complex source radiation patterns, I also suggest to compute diffraction stacking from a characteristic function (CF) instead of stacking the original wave form data. A new CF, which is called in the following mAIC (modified from Akaike Information Criterion) is proposed. I demonstrate that, the performance of the mAIC does not depend on the chosen length of the analyzed time window and that both P- and S-wave onsets can be detected accurately. To avoid cross-talk between P- and S-waves due to inaccurate velocity models, I separate the P- and S-waves from the mAIC function by making use of polarization attributes. Then, eventually the final image function is represented by the largest eigenvalue as a result of the covariance analysis between P- and S-image functions. Before applying diffraction stacking, I also apply seismogram denoising by using Otsu thresholding in the time-frequency domain.
Results from synthetic experiments show that the proposed diffraction stacking provides reliable results even from seismograms with low SNR=1. Tests with different presentations of the synthetic seismograms (displacement, velocity, and acceleration) shown that, acceleration seismograms deliver better results in case of high SNR, whereas displacement seismograms provide more accurate results in case of low SNR recordings. In another test, different measures (maximum amplitude, other statistical parameters) were used to determine the source location in the final image function. I found that the statistical approach is the preferred method particularly for low SNR.
The work flow of my diffraction stacking method was finally applied to local earthquake data from Sumatra, Indonesia. Recordings from a temporary network of 42 stations deployed for 9 months around the Tarutung pull-apart Basin were analyzed. The seismic event locations resulting from the diffraction stacking method align along a segment of the Sumatran Fault. A more complex distribution of seismicity is imaged within and around the Tarutung Basin. Two lineaments striking N-S were found in the middle of the Tarutung Basin which support independent results from structural geology. These features are interpreted as opening fractures due to local extension. A cluster of seismic events repeatedly occurred in short time which might be related to fluid drainage since two hot springs are observed at the surface near to this cluster.
Menschen mit chronisch entzündlichen Darmerkrankungen (CED) leiden unter vielfältigen körperlichen und psychosozialen Einschränkungen. Wie auch bei anderen chronischen Erkrankungen könnten Patientenschulungen ihr psychisches Befinden verbessern (z.B. De Ridder & Schreurs, 2001; Faller, Reusch & Meng, 2011a; Küver, Becker & Ludt, 2008; Schüssler, 1998; Warsi, Wang, LaValley, Avorn & Solomon, 2004). Für CED liegen jedoch nur wenige Schulungsevaluationen vor (z.B. Bregenzer et al., 2005; Mussell, Böcker, Nagel, Olbrich & Singer, 2003; Oxelmark, Magnusson, Löfberg & Hillerås, 2007), deren Aussagekraft i.d.R. durch methodische Mängel eingeschränkt ist. Daher ist die Bedeutung von Schulungsprogrammen für CED-Betroffene weiterhin offen. Überdies gibt es für den deutschen Sprachraum noch keine Schulung, die zu psychischen Verbesserungen führt. Aus diesem Grunde wurde ein 1,5-tägiges Wochenend-Seminar mit medizinischen und psychologischen Inhalten konzeptionalisiert, manualisiert und in der vorliegenden Studie evaluiert.
Zur summativen Evaluation nahmen 181 ambulante CED-Patienten an einer prospektiven, multizentrischen, randomisierten, kontrollierten Studie mit vier Messzeitpunkten teil: vor (T1), zwei Wochen (T2) und drei Monate (T3) nach dem Seminar. Zur 12-Monatskatamnese (T4EG) wurde die Stabilität der Effekte in der Experimentalgruppe (EG; n = 86) überprüft. Die Wartekontrollgruppe (n = 95) erhielt zunächst die Standardbehandlung, also keine Patientenschulung, und konnte an dieser nach der dritten Datenerhebung ebenfalls teilnehmen. Kovarianzanalysen (ANCOVAs) mit Kontrolle für die jeweilige Ausgangslage wurden durchgeführt. Weitere Analysen legten eine Adjustierung für die Krankheitsaktivität zu T1 nahe, weshalb diese als zusätzliche Kovariate in die ANCOVAs aufgenommen wurde. Krankheitsbezogene Ängste und Sorgen (PS-CEDE Gesamtwert zu T3; Krebs, Kachel & Faller, 1998) fungierten als primärer Zielparameter. Zu den sekundären Zielkriterien gehörten Progredienzangst und Angstbewältigung (PA-F-KF und PA-F; Mehnert, Herschbach, Berg, Henrich & Koch, 2006 bzw. Dankert et al., 2003; Herschbach et al., 2005) sowie die Gesundheitskompetenzen Positive Grundhaltung, Aktive Lebensgestaltung und Erwerb von Fertigkeiten und Handlungsstrategien (heiQ; Osborne, Elsworth & Whitfield, 2007; Schuler et al., 2013). Weitere sekundäre Zielparameter waren gesundheitsbezogene Lebensqualität (SF-12; Bullinger & Kirchberger, 1998), Symptome einer Angststörung oder Depression (PHQ-4; Kroenke, Spitzer, Williams & Löwe, 2009; Löwe et al., 2010), Wissen, der Umgang mit der CED bzw. von ihr ausgelösten negativen Gefühlen sowie die Zufriedenheit der Teilnehmenden mit dem Seminar. Von Interesse war außerdem, ob Geschlecht, Alter, Art, Dauer oder Aktivität der Erkrankung vor der Schulung einen Einfluss auf die genannten Variablen hatten und ob für sie differentielle Wirksamkeitseffekte bestanden. Darüber hinaus wurden krankheitsbezogene Ängste und Sorgen von ungeschulten Studienteilnehmern untersucht.
Zwei Wochen und drei Monate nach der Schulung ließen sich im Vergleich von Experimental- und Kontrollgruppe signifikante, mittlere bis große Effekte auf krankheitsbezogene Ängste und Sorgen, Progredienzangst und deren Bewältigung sowie eine Positive Grundhaltung der CED gegenüber erzielen (stets p ≤ .001). Außerdem kam es zu beiden Messzeitpunkten zu signifikanten, großen Interventionseffekten auf den Erwerb von Fertigkeiten und Handlungsstrategien im Umgang mit der Erkrankung, das Wissen um sie und den Umgang mit ihr (stets p < .001) sowie zu moderaten Effekten auf den Umgang mit CED-bedingten negativen Gefühlen (T2: p = .001; T3: p = .008). Alle beschriebenen Effekte waren auch nach zwölf Monaten noch stabil. Für Aktive Lebensgestaltung, gesundheitsbezogene Lebensqualität sowie Angst- und Depressionssymptomatik konnten keine Schulungseffekte nachgewiesen werden.
Die zusätzliche Kontrolle für die Krankheitsaktivität zu T1 führte zu keinen wesentlichen Änderungen in den Ergebnissen. Auch bei den Subgruppenanalysen hatte die Krankheitsaktivität keinen relevanten Einfluss auf die Wirksamkeit der Schulung. Gleiches gilt für Geschlecht, Alter, Art und Dauer der CED. Mit Ausnahme der Krankheitsaktivität deuteten dies bereits die zur Baseline durchgeführten t-Tests an, bei denen insgesamt nur sehr wenige signifikante, höchstens moderate Unterschiede zwischen den einzelnen Subgruppen auftraten.
Sowohl bei der formativen als auch der summativen Evaluation zeigte sich überdies die hohe Zufriedenheit der Teilnehmenden mit der Schulung. Neben der Akzeptanz konnte außerdem die Durchführbarkeit bestätigt werden. Die Auswertung der Ängste und Sorgen der Studienteilnehmenden lieferte zudem Hinweise für die Entwicklung und Modifikation von Interventionen für CED-Betroffene.
Es lässt sich festhalten, dass für die hier evaluierte Schulung für CED-Patienten ein Wirksamkeitsnachweis erbracht werden konnte und sie sehr positiv von den Teilnehmenden bewertet wurde. Sie führte sowohl kurz-, mittel- als auch langfristig zu substantiellen Verbesserungen in psychischer Belastung, Selbstmanagement-Fähigkeiten, der Bewältigung der Erkrankung sowie im Wissen und war gleichermaßen wirksam bei Betroffenen, die sich in Geschlecht, Alter, Art, Dauer oder Aktivität ihrer CED unterschieden.
All life-sustaining processes are ultimately driven by thousands of biochemical reactions occurring in the cells: the metabolism. These reactions form an intricate network which produces all required chemical compounds, i.e., metabolites, from a set of input molecules. Cells regulate the activity through metabolic reactions in a context-specific way; only reactions that are required in a cellular context, e.g., cell type, developmental stage or environmental condition, are usually active, while the rest remain inactive. The context-specificity of metabolism can be captured by several kinds of experimental data, such as by gene and protein expression or metabolite profiles. In addition, these context-specific data can be assimilated into computational models of metabolism, which then provide context-specific metabolic predictions.
This thesis is composed of three individual studies focussing on context-specific experimental data integration into computational models of metabolism. The first study presents an optimization-based method to obtain context-specific metabolic predictions, and offers the advantage of being fully automated, i.e., free of user defined parameters. The second study explores the effects of alternative optimal solutions arising during the generation of context-specific metabolic predictions. These alternative optimal solutions are metabolic model predictions that represent equally well the integrated data, but that can markedly differ. This study proposes algorithms to analyze the space of alternative solutions, as well as some ways to cope with their impact in the predictions.
Finally, the third study investigates the metabolic specialization of the guard cells of the plant Arabidopsis thaliana, and compares it with that of a different cell type, the mesophyll cells. To this end, the computational methods developed in this thesis are applied to obtain metabolic predictions specific to guard cell and mesophyll cells. These cell-specific predictions are then compared to explore the differences in metabolic activity between the two cell types. In addition, the effects of alternative optima are taken into consideration when comparing the two cell types. The computational results indicate a major reorganization of the primary metabolism in guard cells. These results are supported by an independent 13C labelling experiment.
Mathematical models of bacterial growth have been successfully applied to study the relationship between antibiotic drug exposure and the antibacterial effect. Since these models typically lack a representation of cellular processes and cell physiology, the mechanistic integration of drug action is not possible on the cellular level. The cellular mechanisms of drug action, however, are particularly relevant for the prediction, analysis and understanding of interactions between antibiotics. Interactions are also studied experimentally, however, a lacking consent on the experimental protocol hinders direct comparison of results. As a consequence, contradictory classifications as additive, synergistic or antagonistic are reported in literature.
In the present thesis we developed a novel mathematical model for bacterial growth that integrates cell-level processes into the population growth level. The scope of the model is to predict bacterial growth under antimicrobial perturbation by multiple antibiotics in vitro.
To this end, we combined cell-level data from literature with population growth data for Bacillus subtilis, Escherichia coli and Staphylococcus aureus. The cell-level data described growth-determining characteristics of a reference cell, including the ribosomal concentration and efficiency. The population growth data comprised extensive time-kill curves for clinically relevant antibiotics (tetracycline, chloramphenicol, vancomycin, meropenem, linezolid, including dual combinations).
The new cell-level approach allowed for the first time to simultaneously describe single and combined effects of the aforementioned antibiotics for different experimental protocols, in particular different growth phases (lag and exponential phase). Consideration of ribosomal dynamics and persisting sub-populations explained the decreased potency of linezolid on cultures in the lag phase compared to exponential phase cultures. The model captured growth rate dependent killing and auto-inhibition of meropenem and - also for vancomycin exposure - regrowth of the bacterial cultures due to adaptive resistance development. Stochastic interaction surface analysis demonstrated the pronounced antagonism between meropenem and linezolid to be robust against variation in the growth phase and pharmacodynamic endpoint definition, but sensitive to a change in the experimental duration.
Furthermore, the developed approach included a detailed representation of the bacterial cell-cycle. We used this representation to describe septation dynamics during the transition of a bacterial culture from the exponential to stationary growth phase. Resulting from a new mechanistic understanding of transition processes, we explained the lag time between the increase in cell number and bacterial biomass during the transition from the lag to exponential growth phase. Furthermore, our model reproduces the increased intracellular RNA mass fraction during long term exposure of bacteria to chloramphenicol.
In summary, we contribute a new approach to disentangle the impact of drug effects, assay readout and experimental protocol on antibiotic interactions. In the absence of a consensus on the corresponding experimental protocols, this disentanglement is key to translate information between heterogeneous experiments and also ultimately to the clinical setting.