Occurrence, distribution and behavior of hydrophilic ethers in the aquatic environment
Daria Katarzyna Demers-Stępień
- The objective of the present doctoral thesis was to investigate the occurrence, distribution, and behaviour of six hydrophilic ethers: ethyl tert-butyl ether (ETBE), 1,4-dioxane, ethylene glycol dimethyl ether (monoglyme), diethylene glycol dimethyl ether (diglyme), triethylene glycol dimethyl ether (triglyme), and tetraethylene glycol dimethyl ether (tetraglyme) in surface-, waste-, ground- and drinking water samples. Solid phase extraction and gas chromatography/mass spectrometry were used to analyze the six hydrophilic ethers. Altogether more than 150 surface water samples, almost 100 of each groundwater and wastewater samples, and 10 raw and drinking water samples were analyzed during the research project.
Initially, the method was validated in order to simultaneously determine the analytes of interest in various aquatic environments. A solid phase extraction method that uses coconut charcoal (Resprep® activated coconut charcoal, Restek) or carbon molecular sieve material (SupelcleanTM Envi-CarbTM Plus, Supelco) for analyte absorption were found suitable for determination of ETBE, 1,4-dioxane, and glymes in surface-, drinking-, ground- and wastewater samples. Precision and accuracy of both methods was demonstrated for all analytes of interest. The recovery of target compounds from the ultrapure water spiked at 1.0 µg L−1 was between 86.8 % and 98.2 %, with relative standard deviation below 6 %. The samples spiked at 10.0 µg L−1 gave slightly higher recovery of 90.6 % to 112.2 % with a relative standard deviation below 3.4 % for each analyte. Detection and quantification limits in ultrapure water and surface waters were furthermore established. The limit of quantitation (LOQ) in ultrapure water ranged between 0.024 µg L−1 to 0.057 µg L−1 using Restek cartridges, and 0.030 µg L−1 to 0.069 µg L−1 using Supelco cartridges. In the surface water samples the calculated LOQ was 0.032 µg L−1 to 0.067µg L−1 using coconut charcoal material and 0.032 µg L−1 to 0.052 µg L−1 using the carbon molecular sieve material. Moreover, stability of the unpreserved and preserved water samples as well as the extracts was determined. Preservation of samples with sodium bisulfate (at 1 gram per Liter) resulted in much better stability of the ethers in water samples. Subsequently, 27 samples obtained from seven surface water bodies in Germany (Rivers Rhine, Lippe, Main, Oder, Rur, Schwarzbach and Wesel-Datteln Canal) were analyzed for the six hydrophilic ethers. ETBE was present in only two surface waters (Rhine River and Wesel-Datteln Canal) with concentrations close to the LOQ (up to 0.065 µg L−1). 1,4-Dioxane was detected in all of the water samples at concentrations reaching 1.93 µg L–1. Monoglyme was identified only in the Main and Rhine Rivers at the maximum concentration of 0.114 µg L–1 and 0.427 µg L–1, respectively. Very high concentrations (up to 1.73 µg L−1) of diglyme, triglyme, and tetraglyme were detected in the samples from the Oder River. These glymes were also detected in the Rhine River; however the concentrations did not exceed 0.200 µg L–1. Furthermore, tetraglyme was detected in the Main River at an average concentration of 0.409 µg L–1 (n = 6) and in one sample from the Rur River at 0.192 µg L–1.
Four sampling campaigns were conducted at the Oderbruch polder between October 2009 and May 2012, in order to study the behavior of the hydrophilic ethers and organophosphates during riverbank filtration and in the anoxic aquifer. Moreover the suitability of these target compounds was assessed for their use as groundwater organic tracers. At the time of each sampling campaign, concentrations of triglyme and tetraglyme in the Oder River were between 20–185 ng L–1 (n = 4) and 273¬–1576 ng L–1 (n = 4). Monoglyme, diglyme, and 1,4-dioxane were analyzed only during the two last sampling campaigns. At that time, the concentration of diglyme in Oder River was 65¬–94 ng L-1 (n = 2) and 1,4-dioxane 1610¬–3290 ng L–1 (n = 2). In the drainage ditch, following bank filtration, concentrations of ethers ranged between 1090 ng L–1 and 1467 ng L–1 for 1,4-dioxane, 23¬ng L–1 and 41 ng L–1 for diglyme, 37 ng L–1 and 149 ng L–1 for triglyme, and 496 ng L–1 and 1403 ng L–1 for tetraglyme. In the anoxic aquifer, 1,4-dioxane showed the greatest persistence during the groundwater passage. At the distance of 1150 m from the river and an estimated groundwater age of 41.9 years, a concentration above 200 ng L−1 was detected. A positive correlation was found for the inorganic tracer chloride (Cl−) with 1,4-dioxane and tetraglyme. Similarities in the behavior of Cl− and the organic compound suggested that 1,4-dioxane and tetraglyme are controlled by the same hydraulic process and therefore can be used as additional tracers to study the dynamics of the groundwater system. These results show that high concentrations of ethers are present in the surface water and are not removed during bank filtration processes. Moreover, the hydrophilic ethers persist in the anoxic aquifer and little or no degradation is expected, supporting, their possible application as organic tracers.
A separate sampling project was conducted for 1,4-dioxane that focused primarily on its fate in the aquatic environment. This study provided missing information on the extent of water pollution with 1,4-dioxane is Germany. Numerous waste-, surface-, ground- and drinking water samples were collected in order to determine the persistence of 1,4-dioxane in the aquatic environment. The occurrence of 1,4-dioxane was determined in wastewater samples from four municipal sewage treatment plants (STP). The influent and effluent samples were collected during weekly campaigns. The average influent concentrations in all four plants ranged from 262 ± 32 ng L−1 to 834 ± 480 ng L−1, whereas the average effluents concentrations were between 267 ± 35 ng L−1 and 62,260 ± 36,000 ng L−1. The source of increased 1,4-dioxane concentrations in one of the effluents was identified to originate from impurities in the methanol used in the postanoxic denitrification process. Spatial and temporal distribution of 1,4-dioxane in the river Main, Rhine, and Oder was also examined. Concentrations reaching 2,200 ng L−1 in the Oder River, and 860 ng L−1 in both Main and Rhine River were detected. The average load during the sampling was estimated to be 6.5 kg d−1 in the Main, 34.1 kg d−1 in the Oder, and 134.5 kg d−1 in the Rhine River. In all of the sampled rivers, concentrations of 1,4-dioxane increased with distance from the mouth of the river and were found to negatively correlate with the discharge of the river. In order to determine if 1,4-dioxane can reach drinking water supplies, samples from a Rhine River bank filtration site and potable water from two drinking water production facilities were analyzed for the presence of 1,4-dioxane in the raw water and finished potable water. The raw water (following bank filtration) contained 650 ng L−1 to 670 ng L−1 of 1,4-dioxane, whereas the concentration in the finished drinking water fell only to 600 ng L−1 and 490 ng L−1, respectively.
During the final project, investigations of the source identification of high glyme concentrations in the Oder River were carried out. During four sampling campaigns between January, 2012 and April, 2013, 50 samples from the Oder River in the Oderbruch region and Poland were collected. During the first two samplings in the Oderbruch polder, glymes were detected at concentration reaching 0.07 µg L-1 (diglyme), 0.54 µg L−1 (triglyme) and 1.73 µg L−1 (tetraglyme) in the Oder River. The extensive sampling campaign of the Oder River (about 500 km) in Poland helped to identify the area of possible glyme entry into the river. During that sampling the maximum concentrations of triglyme and tetraglyme were 0.46 µg L−1 and 2.21 µg L−1, respectively. A closer investigation of the identified area of pollution, helped to determine the possible sources of glymes in the Oder River. Hence, the final sampling focused on the Kaczawa River, a left tributary of the Oder River and Czarna Woda, a left tributary of Kaczawa River. Moreover, samples from an industrial wastewater treatment plant were collected. Samples from Czarna Woda stream and Kaczawa River contained even higher concentrations of diglyme, triglyme, and tetraglyme, reaching 5.18 µg L−1, 12.87 µg L−1 and 80.81 µg L−1, respectively. Finally, three water samples from a wastewater treatment plant receiving influents from a copper smelter were analyzed. Diglyme, triglyme, and tetraglyme were present at an average concentration of 569 µg L−1, 4300 µg L−1, and 65900 µg L−1, respectively in the wastewater. Further research helped to identify the source of the glymes in the wastewater. The gas desulfurization process – Solinox implemented in the nearby copper smelter uses glymes as physical absorption medium for sulfur dioxide.
Results of this doctoral research provide important information about the occurrence, distribution, and behavior of hydrophilic ethers: 1,4-dioxane, monoglyme, diglyme, triglyme, and tetraglyme in the aquatic environment. A method capable of analyzing a wide range of ether compounds: from a volatile ETBE to a high molecular weight tetraglyme was validated. 1,4-Dioxane and tetraglyme were found to be applicable as organic tracers, since they are not easily attenuated during bank filtration and the anoxic groundwater passage. The extent of water pollution with 1,4-dioxane was shown in waste-, surface-, ground-, and drinking waters. One source of extremely high concentrations of 1,4-dioxane in a municipal sewage treatment plant applying postanoxic denitrification was identified, however more information is needed on the entry of 1,4-dioxane into surface waters. Moreover, 1,4-dioxane was present in drinking water samples from river bank filtration, which demonstrates its persistence in the aquatic environment and its low degradation potential during bank filtration and subsequent water treatment. Furthermore, this was the first study that focused primarily on identifying sources of glymes in surface waters. Glymes find a widespread use in industrial sectors, hence establishing their origin in the surface water is difficult (as with 1,4-dioxane). In this work, a gas desulphurization process was identified to be a dominating source of glyme pollution in the Oder River.
Large-scale parallelized learning of nonlinear sparse coding models
- The human brain is an unparalleled system: Through millions of years of evolution and during a lifespan of learning, our brains have developed remarkable abilities for dealing with incoming sensory data, extracting structure and useful information, and finally drawing the conclusions that result in the actions we take. Understanding the principles behind this machinery and building artificial systems that mimic at least some of these capabilities is a long standing goal in both the scientific and the engineering communities. While this goal still seems unreachable, we have seen tremendous progress when it comes to training data-driven algorithms on vast amounts of training data, e.g. to learn an optimal data model and its parameters in order to accomplish some task. Such algorithms are now omnipresent: they are part of recommender systems, they perform speech recognition and generally build the foundation for many semi-autonomous systems. They start to be integral part of many technical systems modern technical societies rely on for their everyday functioning. Many of these algorithms were originally inspired by biological systems or act as models for sensory data processing in mammalian brains. The response properties of a certain population of neurons in the first stages of the mammalian visual pathway, for example, can be modeled by algorithms such as Sparse Coding (SC), Independent Component Analysis (ICA) or Factor Analysis (FA). These well established learning algorithms typically assume linear interactions between the variables of the model. Most often these relationships are expressed in the form of a matrix-vector products between a matrix with learned dictionary-elements (basis vectors as column vectors) and the latent variables of these models. While on the one hand this linear interaction can sometimes be justified by the physical process for which the machine learning model is proposed, it is on the other hand often chosen just because of its mathematical and practical convenience. From an optimal coding point of view though, one would generally expect that the ideal model closely reflect the core interactions of the system it is modeling. In vision for example, one of the dominant processes giving rise to our sensory percepts are occlusions. Occluding objects are omnipresent in visual scenes and it would not be surprising if the mammalian visual system would be optimized to process occluding structures in the visual data stream. Yet, the established mathematical models of the first stages of the visual processing path (like, e.g., SC, ICA or FA) all assume linear interactions between the active image components. In this thesis we will discuss new models that aim to approximate the effects of occluding components by assuming nonlinear interactions between their activated dictionary elements. We will present learning algorithms that infer optimal parameters for these models given data. In the experiments, we will validate the algorithms on artificial ground truth data and demonstrate their ability to recover the correct model parameters. We will show that the predictions made by these nonlinear models correspond better to the experimental data measured in-vivo than the predictions made by the established linear models. Furthermore, we systematically explore and compare a large space of plausible combinations of hyperparameters and preprocessing schemes in order to eliminate any effects of artefacts on the observed results. Training nonlinear sparse coding models is computationally more demanding than training linear models. In order to perform the numerical experiments described in this thesis we developed a software framework that facilitates the implementation of massive parallel expectation maximization (EM) based learning algorithms. This infrastructure was used for all experiments described in here, as well as by collaborators in projects we will not discuss. Some of the experiments required more than 1017 floating point operations and were run on a computer cluster running on up to 5000 CPU Cores in parallel. Our parallel framework enabled these experiments to be performed.
Sportbezogene Klassenfahrten als Medium der sozialen Integration : eine empirische Untersuchung am Beispiel einer Skifahrt in der Jahrgangsstufe 7
- Es wird allgemein vermutet, dass Klassenfahrten bei den Schülern nachhaltige Veränderungen bewirken können und nur wenige empirische Befunde belegen die Wirksamkeit von Klassenfahrten. Diese defizitäre Forschungslage aufgreifend, beschäftigt sich die vorliegende Arbeit mit der sozial-integrativen Wirkung einer sportbezogenen Klassenfahrt (Skifahrt) auf empirischer Grundlage.
Mit Hilfe der Desintegrationstheorie von Anhut & Heitmeyer (2000) lässt sich das Konstrukt „Integration“ in allgemeinerer Form über das antinomische Begriffspaar „Anerkennung vs. Ablehnung“ operationalisieren, wobei zwischen positionaler, moralischer und emotionaler Anerkennung bzw. Ablehnung unterschieden werden kann. Neben individuellen Merkmalen erfolgt die Vergabe und Verweigerung von Anerkennung über kollektive Merkmale, die auf Zugehörigkeit zu einer Gruppe beruht. Im pädagogischen Kontext der Schulklasse ist daher von besonderem Interesse, wie sich die Anerkennungsverhältnisse zwischen Gruppen verändern, denen besondere Potenziale für heterogenitätsbedingte Ablehnung zugeschrieben wird (vgl. Gerecke, 2010). Hypothetisch sind dies Mädchen „vs.“ Jungen, Jugendliche mit „vs.“ Jugendliche ohne Migrationshintergrund und bezüglich Klassenfahrten die Gruppe der Schüler, die nicht teilnehmen konnten „vs.“ der Gruppe derer, die teilgenommen haben. Auf dieser Grundlage beschäftigt sich die vorliegende Arbeit mit den Effekten sportbezogenen Klassenfahrten auf die soziale Integration operationalisiert in Anerkennungsverhältnissen.
Mittels eines soziometrischen Wahlverfahrens wurden die Anerkennungs- und Ablehnungsverhältnisse von vier Schulklassen (N=95) zu drei Messzeitpunkten (Eingangs-, Ausgangs- und Behaltenstest nach sechs Wochen) computergestützt erhoben.
Die Betrachtung der Gesamtgruppe zeigt eine Steigerung der positiven Wahlen (eta²=0,210) bei einer gleichzeitigen Reduktion der negativen Wahlen (eta²=0,167). Diese Entwicklung ist über Post-hoc-Einzelvergleiche auf eine signifikante Veränderung innerhalb des Treatmentzeitraumes (ET AT) zurückzuführen. Das Intervall AT-BT nach Abschluss der Klassenfahrt ist nicht signifikant, so dass auf eine zeitliche Stabilität der Ergebnisse geschlossen werden kann. Allerdings sind große Unterschiede zwischen den einzelnen Klassen festzustellen, die nicht teilweise nicht mit dem Gesamtergebnis übereinstimmen. In der differenzierten Betrachtung der heterogenitätsbedingten Unterschiede ist in erster Linie ein Geschlechtereffekt zu erkennen. Insbesondere die positiven und negativen Wahlen zwischen Schülern verschiedenen Geschlechts verändern sich signifikant. Aber auch hier zeigen sie die bereits dargestellten klassenspezifischen Differenzen.
Während der Teilnahmestatus keinen Einfluss auf die Vergabe von negativen und positiven Wahlen besitzt, beeinflusst der Migrationsstatus hingegen die positiven Wahlen signifikant.
Mit Blick auf die theoretischen Grundlagen dieser Arbeit kann der Anstieg der positiven Wahlen als Zuwachs von Anerkennung und der Rückgang negativer Wahlen als eine Reduktion von Ablehnung interpretiert werden, wobei sich kein einheitliches Bild auf Klassenebene ergibt.
Anhut, R. & Heitmeyer, W. (2000). Desintegration, Konflikt und Ethnisierung. Eine Problemanalyse und theoretische Rahmenkonzeption. In W. Heitmeyer (Hrsg.), Bedrohte Stadtgesellschaft. Soziale Desintegrationsprozesse und ethnisch-kulturelle Konfliktkonstellationen (S. 17–73). Weinheim: Juventa-Verlag.
Gerecke, P. (2010). Heterogenitätsbedingte Unterschiede zwischen Ingroup- und Outgroup-Anerkennung bzw. -Ablehnung im Sportunterricht. Eine empirische Studie zum integrativen Einfluss des Kooperativen Lernens. Dissertation. Frankfurt am Main: Johann-Wolfgang Goethe Universität.
The Silicon Tracking System of the CBM experiment at FAIR : development of microstrip sensors and signal transmission lines for a low-mass, low-noise system
- In this thesis, different physical and electrical aspects of silicon microstrip sensors and low-mass multi-line readout cables have been investigated. These silicon microstrip sensors and readout cables will be used in the Silicon Tracking System (STS) of the fixed-target heavy-ion Compressed Baryonic Matter (CBM) experiment which is under development at the upcoming Facility for Antiproton and ion Research (FAIR) in Darmstadt, Germany. The highly segmented low-mass tracking system is a central CBM detector system to resolve the high tracking densities of charged particles originating from beam-target interactions. Considering the low material budget requirement the double-sided silicon microstrip detectors have been used in several planar tracking stations. The readout electronics is planned to be installed at the periphery of the tracking stations along with the cooling system. Low-mass multi-line readout cables shall bridge the distance between the microstrip sensors and the readout electronics. The CBM running operational scenario suggests that some parts of the tracking stations are expected to be exposed to a total integrated particle fluence of the order of 1e14 neq/cm2. After 1e14 neq/cm2 the damaged modules in the tracking stations will be replaced. Thus radiation hard sensor is an important requirement for the sensors. Moreover, to cope with the high reaction rates, free-streaming (triggerless) readout electronics with online event reconstruction must be used which require high signal-to-noise (SNR) ratio (i.e., high signal efficiency, low noise contributions). Therefore, reduction in noise is a major goal of the sensor and cable development.
For better insight into the different aspects of the silicon microstrip sensors and multi-line readout cables, the simulation study has been performed using SYNOPSYS TCAD tools. 3D models of the silicon microstrip sensors and the readout cables were implemented which is motivated by the stereoscopic construction of the silicon microstrip sensors. For the evaluation of the performance of the silicon microstrip sensors in the harsh radiation environment during experimental operation, a radiation damage model has been included. It reproduces the behavior of the irradiated CBM prototype sensors. In addition to the static characteristics, the interstrip parameters relevant to understand strip isolation and cross-talk issues have been extracted. The transient simulations have been performed to estimate the charge collection performance of the irradiated sensors. The signal transmission in the readout cables has been evaluated with the finite element simulation tool RAPHAEL. Based on the performance of the front-end electronics used for early prototyping in the CBM experiment, capacitive and resistive noise contributions from the silicon microstrip sensors and multi-line readout cables have been extracted.
To validate the aforementioned simulations, numerous tests have been performed both on the multi-line readout cables and silicon microstrip sensors. Characterizations of multi-line readout cables and silicon microstrip sensors in laboratory conditions have been found to agree reasonably well with the simulations. Considering the expected radiation environment the behavior of silicon microstrip sensors have been studied especially in terms of noise and charge collection efficiency. Source-scan of the silicon microstrip sensors using 241Am is presented. In order to test a first system of detector stations including the data acquisition system, slow control and online monitoring software and for track reconstruction, in-beam tests have been performed at the COSY synchrotron of the Research Center Juelich, Germany. Further, different design parameters have been suggested to improve the sensor and readout cable design on the basis of the simulations and the measurements. Many of these parameters have been implemented in the new prototypes under production. These new prototypes will be tested in-beam by the end of 2013.
Analysis of splicing sensitive microarrays
- Due to recent technical developments, it became evident that the mammalian transcriptome is much more complex than originally expected. Alternative splicing(AS) and the transcription of long non-coding RNAs (lncRNAs) are two phenomenas which have been greatly underestimated in their frequency. Nowadays it is accepted that almost every gene has at least one alternative isoform and the number of lncRNAs exceeds the one of protein-coding genes.
We built user-friendly web interfaces which can process Affymetrix GeneChip Exon 1.0 ST Arrays (exon arrays) and GeneChip Gene 1.0 ST Arrays (gene arrays)for the analysis of alternative splicing events. Results are presented with detailed annotation information and graphics to identify splice events and to facilitate biological validations. Based on two studies using exon arrays, we show how our tools were used to profile genome-wide splicing changes under silencing of Jmjd6 and under hypoxic conditions. Since gene arrays are not intended for AS analysis originally, we demonstrated their applicability by profiling alternative splicing events during embryonic heart development.
To measure lncRNAs expressions with exon arrays, we completely re-annotation all probes and built a lncRNA specific annotation. To demonstrate the applicability of exon arrays in combination with our annotation, we profiled the expression of tens of thousands of lncRNAs. Further, our custom annotation allows for a detailed inspection of lncRNAs and to distinguish between isoforms, as we validated by RTPCR.
To allow for a general usage to the research community, we integrated the annotation in an easy-to-use web interface, which provides various helpful features for the analysis of lncRNAs.
Identification and characterization of selected secondary metabolite biosynthetic pathways from Xenorhabdus nematophila
Learning sequences of actions : infant experiments and neural network models
- In our daily life, we carry out lots of tasks like typing, playing tennis, and playing the piano, without even noticing there is sequence learning involved. No matter how simple or complex they are, these tasks require the sequential planning and execution of a series of movements. As an ability of primary importance in one’s life, and an ability that everyone manages to learn, action-sequence learning has been studied by researchers from different fields: psychologists, neurophysiologists as well as roboticists. In the concept of sequence learning, perceptual learning and motor learning, implicit and explicit learning have been studied and discussed independently.
We are interested in infancy research, because infants, with underdeveloped brain functions and with limited motor ability, have little experience with the world and not yet built internal models as presumption of how to interpret the world. A series of infant experiments in the 1980s provided evidence that infants can rapidly develop anticipatory eye movements for visual events. Even when infants have no control of those spatial-temporal patterns, they can respond actually prior to the onset of the visual event, referred as "Anticipation".
In this work, we applied a gaze-contingent paradigm using real-time eye tracking to put 6- and 8-month-old infants in direct control of their visual surroundings. This paradigm allows the infant to change an image on a screen by looking at a peripheral red disc, which functions as a switch. We found that infants quickly learn to perform eye movements to trigger the appearance of new stimuli and that they anticipate the consequences of their actions in an early stage of the experiment.
Attention-shift from learning one stimulus to the next novel stimulus is important in sequence learning. In the test phase of infant visual habituation with two objects, we propose a new theory of explaining the familiarity-to-novelty shift. In our opinion an infant’s interest in a stimulus is related to its learning progress, the improvement of performance. As a consequence, infants prefer the stimulus which their current learning progress is maximal for, naturally giving rise to a familiarity-to-novelty shift in certain situations. Our network model predicts that the familiarity-to-novelty-shift only emerges for complex stimuli that produce bell-shaped learning curves after brief familiarization, but does not emerge for simple stimuli that produce exponentially decreasing learning curves or for long familiarization time, which is consistent with experimental results. This research suggests the infant's interest in a stimulus may be related to its current learning progress. This can give rise to a dynamic familiarity-to-novelty shift depending on both the infant's learning efficiency and the task complexity.
We know that for both infants and adults, the performance on certain motor-sequence tasks can be improved through practice. However, adults usually have to perform complex tasks in complicated environments; for example, learning multiple tasks is unavoidable in our daily life. In existing research, learning multiple tasks showed puzzling and seemingly contradictory results. On the one hand, a wide variety of proactive and retroactive interference effects have been observed when multiple tasks have to be learned. On the other hand, some studies have reported facilitation and transfer of learning between different tasks.
In order to find out the interaction between multiple-task learning, and to find an optimal training schedule, we use a recurrent neural network to model a series of experiments on movement sequence learning. The network model learns to carry out the correct movement sequences through training and reproduces differences between training schedules such as blocked training vs. random training in psychophysics experiments. The network model also shows striking similarity to human performance, and makes prediction for tasks similarity and different training schedules.
In conclusion, the thesis presents learning sequences of actions in infants and recurrent neural networks. We carried out a gaze-contingent experiment to study infants’ rapid anticipation of their own action outcomes, and we also constructed two recurrent neural network models, with one model explaining infant attention shift in visual habituation, and the other model directing to task similarity and training schedule in motor sequence control in adults.
Methodenoptimierung zur qualitativen und quantitativen Anwendung wenig spezifischer Proteasen in der Proteomforschung
- Die Proteomforschung wurde die letzten beiden Dekaden maßgeblich durch die Massenspektrometrie geprägt und vorangetrieben. Ohne die Ionisationstechniken MALDI und ESI wäre die Analyse von Peptiden und Proteinen nicht in dem Maße möglich. Durch das Zusammenspiel zwischen Probenvorbereitung und effektiven Trennmethoden mit hochauflösenden Massenspektrometern und Auswertungssoftware können heute problemlos komplexe Proteinmischungen oder ganze Proteome untersucht werden.
Um Proteine in Peptide zu schneiden, wird in den allermeisten Fällen die Protease Trypsin verwendet, deren Eigenschaften in vielerlei Hinsicht die bestmögliche Lösung für die nachfolgende Analyse mit Massenspektrometern bieten. Allerdings stößt die Anwendbarkeit dieses Enzyms bei der Analyse von einigen Proteinen oder Proteinklassen wie Membranproteinen an ihre Grenzen, da nur sehr wenige potentielle Schnittstellen vorhanden sind. In solchen Fällen wurden eine Reihe von weniger spezifischen Enzymen wie Chymotrypsin, Proteinase K oder Elastase in den vergangenen Jahren genutzt, die Proteine auch in für Trypsin weniger gut zugänglichen Bereichen wie Transmembranhelices, in massenspektrometrisch analysierbare Peptide spalten können.
Allerdings stellen die wenig spezifischen Enzyme und die von ihnen generierten Peptide die Massenspektrometrie vor neue Herausforderungen. Für eine Identifizierung benötigen die Peptide eine sehr hohe Massengenauigkeit, daneben sind insbesondere bei der Verwendung von MALDI-Massenspektrometern neutrale und sehr saure Peptide schwerer ionisierbar und analysierbar als basische.
Genügte es bis vor einigen Jahren, nur die Identität einzelner Proteine in komplexen Proben zu bestimmen, hat sich die Fragestellung mittlerweile einem Wandel unterzogen. Heute ist man daran interessiert, wie viel eines bestimmten Proteins vorliegt, besonders im Vergleich mit anderen, unterschiedlich behandelten Proben ist die Regulation von Proteinen von Interesse. Zum Quantifizieren stehen viele unterschiedliche Methoden zur Verfügung. Eine solche stellen die isobaren Derivatisierungsreagenzien TMT und iTRAQ dar, mit denen unterschiedliche Proben nach Peptidfragmentierung quantifiziert werden können.
Fast alle Arbeiten zur Quantifizierung in der Vergangenheit benutzten Trypsin als Protease.
Im Zuge dieser Arbeit sollten die Vorteile, die durch die Verwendung von Elastase bei der Identifizierung von Membranproteinen bereits gezeigt werden konnten, auf die Quantifizierung mit TMT erweitert werden.Wurde in der Vergangenheit noch in manchen Publikationen davon abgeraten, Elastase zu verwenden,weil die Nutzbarkeit der dabei gebildeten komplexen Peptidmischungen in Frage gestellt wurde, konnte in dieser Arbeit gezeigt werden, dass Elastase wie auch Trypsin sich eignen, als Enzym für Quantifizierungsexperimente verwendet zu werden. Dies wurde an Modellproteinen evaluiert und dann auf komplexe Membranproben von Hefezellen erweitert.
Bei Vorexperimenten zur Derivatisierung mit TMT wurde desweiteren festgestellt, dass Peptidklassen, die zuvor nur mit ESI als Ionisationsmethode identifiziert werden konnten, durch die Derivatisierung nun auch mit MALDI zugänglich waren. Die dadurch analysierten kleinen, hydrophoben und sehr sauren Peptide lieferten bei der Kombination mit der underivatisierten Probe einen deutlichen Zugewinn in der Sequenzabdeckung der identifizierten Proteine.
Ein weiterer Teil der Arbeit beschäftigt sich mit der nachträglichen Korrektur von gemessenen Peptidmassen über selbst geschriebene Softwarelösungen für verschiedene Massenspektrometer. Es wurde das Ziel verfolgt, eine möglichst hohe Massengenauigkeit und damit hohe Anzahl an Identifizierungen von Proteinen nach Verdau mit wenig spezifischen Proteasen zu erreichen. Weitere Computerprogramme wurden mit dem Ziel geschrieben, den Arbeitsablauf zu erleichtern und zu verbessern.
Für die früher schon beschriebene Kombination zweier Massenspektrometer mit hoher Massengenauigkeit und Auflösung auf der einen Seite und effizienter Peptidfragmentierung auf der anderen Seite konnte durch Veränderung der Instrumentierung und Software nun eine Automatisierbarkeit geschaffen werden, die es ermöglicht, die Methode standardmäßig bei Routineanalysen zu verwenden.
So ergeben sich viele neue Möglichkeiten neben den oft gewählten Standardprotokollen mit der Analyse tryptischer Verdauansätze mittels LC-ESI-MS/MS, die häufig nur der Einfachheit halber und ohne Anpassung an die eigene Zielsetzung gewählt werden.
Die Arbeit zeigt aber auch auf, dass die Verwendung weniger spezifischer Enzyme sowohl eine Optimierung des Arbeitsablaufs als auch eine Datenauswertung benötigt, die die Besonderheiten der Proteasen berücksichtigt. Wenn dies gewährleistet wird, kann vor allem mit dem Zugewinn durch die Derivatisierung mit TMT eine wertvolle Alternative zu Trypsin genutzt werden.
Recombinant measles viruses : use as bivalent vaccine and modulation of their membrane fusion activity
- Life-attenuated measles virus (MV) vaccines have revealed their capacity to routinely induce life-long immunity against MV after just a single or two low-dose injections. Moreover, MV vaccines have been shown to be extensively safe and well tolerated, in general. Thus, MV is a prime candidate for a recombinant vaccine platform to protect also against other pathogens after vaccination. For this purpose, foreign genes can be inserted into additional transcription units (ATU) in recombinant MV genomes so that the encoded foreign proteins are co-expressed with MV proteins in infected cells. These so-called bivalent MV should protect against infection by MV or the pathogen, which the encoded foreign protein had been derived from. Bivalent MVs have already been shown to be effective vaccines against e.g. dengue virus or hepatitis B virus infections by inducing humoral and sometimes also cellular immune responses. In most of these studies, soluble or soluble versions of the pathogens' antigens were used for generation of bivalent MVs.
We hypothesized that the form of the antigen expressed by bivalent MVs is crucial for the potency and constitution of the induced immune responses. Therefore, three different forms of an antigen expressed by bivalent MVs were analyzed, here. The model antigen chosen for this purpose has been the envelope protein (Env) of SIVsmmPBj1.9. In its natural mature form, Env is composed of the surface unit gp120 and the transmembrane unit gp41, which stay non-covalently linked after proteolytic processing of the common precursor protein gp160. However, gp120 can be shed by infected cells or virus particles. Therefore, natural gp160 antigen was used as shedding form. Furthermore, stabilized covalently-linked gp160 variants and soluble gp140 variants were used in this thesis. These different antigen forms were inserted either behind the P or behind the H expression cassettes into the MV genome. The respective bivalent MVs were rescued and characterized. Expression of SIVsmmPBj1.9 Env variants by the bivalent MVs was confirmed by immuno blot and in situ immunoperoxidase assays. Replication curves of bivalent MV showed that growth of MVs expressing the different Env variants was slightly delayed by approximately 24 h compared to control viruses.
For immunization of transgenic, MV-susceptible IFNAR-/--CD46Ge mice, which are the current standard to analyze MV vaccines in a small animal model, an optimal dose of 1x105 TCID50 was determined. For the evaluation of humoral immune responses in transgenic mice, two ELISA systems for the detection of total α-MV and α-SIV antibodies and neutralization assays for detection of neutralizing antibodies against MV and SIV in sera of immunized mice were established. Mice immunized with any of the bivalent MVs showed significant humoral immune responses against MV comparable to those elicited by the parental MV vaccine strain without further genetic modifications. Mice immunized with MVvac2-gp140(P) expressing the soluble gp140 variant revealed highest α-SIV titers with a maximal OD of up to 0.4. Second highest levels of α-SIV antibodies were detected in mice that were immunized with the shedding variants or soluble Env in other positions. MVs expressing the stabilized variants induced only very low α-SIV antibody titers. Neutralizing antibodies directed against SIV could be detected in sera of mice immunized with MVs expressing the soluble or shedding variants, but not in sera of mice immunized with MVs expressing the stabilized variants. In sera of control mice immunized with PBS no antibodies could be detected, as expected. Thus, soluble and shedding antigens induced humoral immune responses, whereas stabilized antigens induced only weak humoral immune responses but no neutralizing antibodies. Analysis of cellular immune responses is still ongoing.
Besides Env, further SIV antigens could be tested for their potency to induce humoral as well as cellular immune responses.
Besides being used as a vaccine platform, recombinant MVs are evaluated as future agent for cancer therapy due to their significant inherent tumor-lytic, so-called oncolytic activity. Currently, the anti-tumoral activity of MV is analyzed in clinical phase I trials. MV strains with high fusion activity are used as oncolytic agents. The fusion protein F of MV strain NSe is highly fusogenic, in contrast to e.g. F of MVwt323, a clone of the pathogenic strain IC-B. Sequence analysis of these two proteins identified one coding nucleotide difference at aa 94 in the F2 domain: a valine (V) in FNSe and a methionine (M) in Fwt323. To evaluate impact of this difference, residues at aa 94 were exchanged. After transient-transfection of MV F and H expression plasmids in receptor-positive cells, V94 in the F2 subunit of FNSe or Fwt323 led to about 6-fold higher fusion activity compared to F proteins with M94. The co-expressed H protein (HNSe or Hwt323) did not influence fusion activity, indicating that the receptor (CD46 or SLAM) bound by H does not quantitatively affect the F proteins' activation. Analysis of F and H showed that formation and transport of MV glycoprotein complexes are not altered by substitution in aa 94 of FNSe or Fwt323.
Furthermore, recombinant MVNSe, MVNSe-F-M94, MVwt323, or MVwt323-F-V94 were rescued. Viral replication revealed slightly higher titers for recombinant MVs expressing M94 in F after 96 h of replication, compared to MVs expressing V94. MVs expressing V94 in F2 showed 2.5-fold higher fusion activity on CD46- and SLAM-positive Vero-hSLAM cells and 2-fold higher fusion activity on B95a cells expressing only SLAM compared to MVs expressing F with M94. Fusion activity of recombinant MVs can thus be modulated by substituting a single aa. V94 in the F protein results in highly fusion active MVs with possibly increased direct cytotoxicity in infected tumors, whereas M94 in F could be associated with decreased fusion activity for therapies, where higher virus titers are required.
The development of infants' action-related object knowledge : deferred imitation and eye tracking studies in 12- and 18-month-olds
- Imitation paradigms are used in various domains of developmental psychological research to assess various cognitive processes such as memory (deferred imitation), action perception and action understanding (mainly direct imitation), as well as categorization and learning about objects (deferred imitation with a change in target objects and generalized imitation). Although these processes are most likely not independent from each other, their relations are still largely unclear. On the one hand, deferred imitation studies have shown that infants' performance improves with increasing age, resulting in the reproduction of more target actions after longer delay intervals. On the other hand, imitation studies focusing on infants' action understanding have found that infants do not necessarily imitate the model's exact actions – actions or action steps that seem to be irrational or irrelevant are omitted by infants under certain circumstances (selective imitation). Additionally, findings of imitation studies that require a transfer of the target actions to novel objects have demonstrated that infants do not only learn about actions, but also about objects, when they engage in imitation.
The present dissertation aims at integrating different perspectives of imitation research by testing 12- and 18-month-old infants in deferred imitation tests consisting of functional vs. arbitrary target actions, and by combining deferred imitation with eye tracking in half of the experiments. A deferred imitation paradigm was chosen to assess memory performance. Systematic variation of target action characteristics enabled the assessment of infants' imitation pattern, i.e., if they would imitate one kind of target actions more frequently than the other. Functionality was chosen as the action characteristic in focus because function is an object's most important property, thus this variation might shed some light on infants' learning about objects in the context of an imitation test. The main goal of the eye tracking experiments was to tackle the relations between infants' visual attention to, and deferred imitation of, different kinds of target actions.
The behavioral experiments revealed that both 12- and 18-month-olds imitated significantly more functional than arbitrary target actions after a delay of 30 minutes. In addition, while 12-month-olds showed a memory effect only for functional actions, 18-month-olds showed a memory effect for both kinds of actions. Thus, 12-month-olds imitated strictly selectively, and 18-month-olds imitated more exactly. This shows that the well established memory effect is modulated by target action functionality, which affects 12- and 18-month-olds' imitation differently. Furthermore, when retested after a two weeks delay, 18-month-olds' performance rates of functional and arbitrary target actions decreased parallel. This suggests that selective imitation is not affected by the duration of the retention interval, and that selection of target actions takes place at an earlier stage of action perception and memory processes.
In the eye tracking experiments, both 12- and 18-month-olds' imitation patterns replicated the findings of the behavioral experiments, showing consistently higher imitation rates of functional than arbitrary target actions. Contrary to this, infants' fixation times to the target actions were not affected by target action functionality. This contrast was supported by statistical analyses that found no clear correspondence between visual attention to and deferred imitation of target actions. This suggests that selective imitation cannot be explained by selective visual attention. Nevertheless, finer-grained analyses of gaze and imitation data in the 18 months old group suggested that infants' increased attention to the social-communicative context of the imitation task was related to more exact imitation, i.e. imitation of not only functional, but also arbitrary target actions.
The findings are discussed against the background of imitation theories, with regard to the relations between different cognitive processes underlying infants' imitation, such as memory, action perception and learning about objects.