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The Venus flytrap, \textit{Dionaea muscipula}, with its carnivorous life-style and its highly
specialized snap-traps has fascinated biologist since the days of Charles Darwin. The
goal of the \textit{D. muscipula} genome project is to gain comprehensive insights into the
genomic landscape of this remarkable plant.
The genome of the diploid Venus flytrap with an estimated size between 2.6 Gbp to
3.0 Gbp is comparatively large and comprises more than 70 % of repetitive regions.
Sequencing and assembly of genomes of this scale are even with state-of-the-art
technology and software challenging. Initial sequencing and assembly of the genome
was performed by the BGI (Beijing Genomics Institute) in 2011 resulting in a 3.7 Gbp
draft assembly. I started my work with thorough assessment of the delivered assembly
and data. My analysis showed that the BGI assembly is highly fragmented and
at the same time artificially inflated due to overassembly of repetitive sequences.
Furthermore, it only comprises about on third of the expected genes in full-length,
rendering it inadequate for downstream analysis.
In the following I sought to optimize the sequencing and assembly strategy to obtain
an assembly of higher completeness and contiguity by improving data quality and
assembly procedure and by developing tailored bioinformatics tools. Issues with
technical biases and high levels of heterogeneity in the original data set were solved
by sequencing additional short read libraries from high quality non-polymorphic DNA
samples. To address contiguity and heterozygosity I examined numerous alternative
assembly software packages and strategies and eventually identified ALLPATHS-LG
as the most suited program for assembling the data at hand. Moreover, by utilizing
digital normalization to reduce repetitive reads, I was able to substantially reduce
computational demands while at the same time significantly increasing contiguity of
the assembly.
To improve repeat resolution and scaffolding, I started to explore the novel PacBio
long read sequencing technology. Raw PacBio reads exhibit high error rates of 15 %
impeding their use for assembly. To overcome this issue, I developed the PacBio
hybrid correction pipeline proovread (Hackl et al., 2014). proovread uses high
coverage Illumina read data in an iterative mapping-based consensus procedure to
identify and remove errors present in raw PacBio reads. In terms of sensitivity and
accuracy, proovread outperforms existing software. In contrast to other correction
programs, which are incapable of handling data sets of the size of D. muscipula
project, proovread’s flexible design allows for the efficient distribution of work load on high-performance computing clusters, thus enabling the correction of the Venus
flytrap PacBio data set.
Next to the assembly process itself, also the assessment of the large de novo draft
assemblies, particularly with respect to coverage by available sequencing data, is
difficult. While typical evaluation procedures rely on computationally extensive
mapping approaches, I developed and implemented a set of tools that utilize k-mer
coverage and derived values to efficiently compute coverage landscapes of large-scale
assemblies and in addition allow for automated visualization of the of the obtained
information in comprehensive plots.
Using the developed tools to analyze preliminary assemblies and by combining my
findings regarding optimizations of the assembly process, I was ultimately able to
generate a high quality draft assembly for D. muscipula. I further refined the assembly
by removal of redundant contigs resulting from separate assembly of heterozygous
regions and additional scaffolding and gapclosing using corrected PacBio data. The
final draft assembly comprises 86 × 10 3 scaffolds and has a total size of 1.45 Gbp.
The difference to the estimated genomes size is well explained by collapsed repeats.
At the same time, the assembly exhibits high fractions full-length gene models,
corroborating the interpretation that the obtained draft assembly provides a complete
and comprehensive reference for further exploration of the fascinating biology of the
Venus flytrap.
„Perspective-taking“ is the ability to put yourself into the place of somebody else. Psychological research distinguishes three kinds of perspective-taking, namely, perceptual (visuo-spatial), affective (empathy), and cognitive (theory of mind) perspective-taking. The last two kinds of perspective-taking are often summarized as “psychological perspective-taking”. This dissertation tackles the question of whether these three kinds of perspective-taking should be conceptualized as independent constructs or as facets of one and the same construct.
Prior research findings concerning this are equivocal. While some authors consider correlations between the different kinds of perspective-taking as too low for a unitary construct, others interpret correlations of the same magnitude as evidence for this. A less arbitrary way of deciding this would be to identify common mechanisms that underlie all kinds of perspective-taking and to examine whether manipulating these mechanisms in psychological experiments affects measures of perceptual, affective, and cognitive perspective-taking in parallel.
In accordance with this reasoning, the present dissertation assumes that the mental self-rotation of the body schema into the physical location of another person, the main mechanism of perceptual perspective-taking, is a common mechanism of all kinds of perspective-taking. Thus, contrary to previous research a unitary construct is not only justified on the grounds of a common central functionality of all kinds of perspective-taking, that is, overcoming one’s egocentrism in favor of an alternative (perceptual, affective or cognitive) point of view, but additionally on the grounds of a common psychological mechanism. From this, the simple hypothesis that inducing visuo-spatial perspective-taking also leads to psychological consequences is derived. This hypothesis was tested in 6 experiments.
In these experiments, participants first had to adopt the visual perspective of another person. To this end, they saw a person sitting at a table with two objects. During every trial, participants had to decide which hand the person would have to use in order to grab one of the two objects. Furthermore, the angular disparity between the participant and the target was manipulated in such a way that during half of the trials the target person was within the same visuo-spatial reference frame as the participant and thus no perspective-taking was necessary to solve the task correctly. During the remaining trials, the target person was sitting in another visuo-spatial reference frame so that the participants had to engage in perspective-taking to solve the task correctly. After every such trial, the target person was imbued with a mental state. This was done using an adapted paradigm for the investigation of the anchoring heuristic. Specifically, participants were asked to answer a trivia question and also saw what the target person from the visuo-spatial perspective-taking task was guessing.
In line with the hypothesis that visuo-spatial perspective-taking leads to psychological outcomes, too, it was found that participants adopted the thoughts of the target person more strongly after visuo-spatial perspective-taking. This was evident in the absolute size of the anchoring effect, as well as the differences between participant and target estimations. Further experiments ruled out sample and stimulus characteristics and task difficulty as alternative explanations for these effects. The last two experiments furthermore established that the effects were specific to constellations where an embodied self-rotation into the target’s perspective was necessary and that the adoption of the target’s thoughts was associated with feelings of similarity.
Taken together, these findings support the theoretically elaborated unitary view of perspective-taking and furthermore distinguish this construct from other related phenomena. In the general discussion, the significance of these findings for research on empathy, theory of mind, and perspective-taking, as well as practical implications are discussed.
The most energetic versions of active galactic nuclei (AGNs) feature two highly-relativistic plasma outflows, so-called jets, that are created in the vicinity of the central supermassive black hole and evolve in opposite directions. In blazars, which dominate the extragalactic gamma-ray sky, the jets are aligned close to the observer's line of sight leading to strong relativistic beaming effects of the jet emission. Radio observations especially using very long baseline interferometry (VLBI) provide the best way to gain direct information on the intrinsic properties of jets down to sub-parsec scales, close to their formation region.
In this thesis, I focus on the properties of three AGNs, IC 310, PKS 2004-447, and 3C 111 that belong to the small non-blazar population of gamma-ray-loud AGNs. In these kinds of AGNs, the jets are less strongly aligned with respect to the observer than in blazars. I study them in detail with a variety of radio astronomical instruments with respect to their high-energy emission and in the context of the large samples in the monitoring programmes MOJAVE and TANAMI. My analysis of radio interferometric observations and flux density monitoring data reveal very different characteristics of the jet emission in these sources. The work presented in this thesis illustrates the diversity of the radio properties of gamma-ray-loud AGNs that do not belong to the dominating class of blazars.
Attention-Deficit/Hyperactivity Disorder (ADHD) is characterized by symptoms of inattentiveness and hyperactivity/impulsivity. Besides, increasing evidence points to ADHD patients showing emotional dysfunctions and concomitant problems in social life. However, systematic research on emotional dysfunctions in ADHD is still rare, and to date most studies lack conceptual differentiation between emotion processing and emotion regulation. The aim of this thesis was to systematically investigate emotion processing and emotion regulation in adult ADHD in a virtual reality paradigm implementing social interaction. Emotional reactions were assessed on experiential, physiological, and behavioral levels.
Experiment 1 was conducted to develop a virtual penalty kicking paradigm implying social feedback and to test it in a healthy sample. This paradigm should then be applied in ADHD patients later on. Pleasant and unpleasant trials in this paradigm consisted of hits respectively misses and subsequent feedback from a virtual coach. In neutral trials, participants were teleported to different spots of the virtual stadium. Results indicated increased positive affectivity (higher valence and arousal ratings, higher zygomaticus activations, and higher expression rates of positive emotional behavior) in response to pleasant compared to neutral trials. Reactions to unpleasant trials were contradictory, indicating increased levels of both positive and negative affectivity, compared to neutral trials. Unpleasant vs. neutral trials revealed lower valence ratings, higher arousal ratings, higher zygomaticus activations, slightly lower corrugator activations, and higher expression rates of both positive and negative emotional behavior. The intensity of emotional reactions correlated with experienced presence in the virtual reality.
To better understand the impact of hits or misses per se vs. hits or misses with coach feedback healthy participants’ emotional reactions, only 50% of all shots were followed by coach feedback in experiment 2. Neutral trials consisted of shots over the free soccer field which were followed by coach feedback in 50 % of all trials. Shots and feedback evoked more extreme valence and arousal ratings, higher zygomaticus activations, lower corrugator activations, and higher skin conductance responses than shots alone across emotional conditions. Again, results speak for the induction of positive emotions in pleasant trials whereas the induction of negative emotions in unpleasant trials seems ambiguous. Technical improvements of the virtual reality were reflected in higher presence ratings than in experiment 1.
Experiment 3 investigated emotional reactions of adult ADHD patients and healthy controls after emotion processing and response-focused emotion regulation. Participants successively
went through an ostensible online ball-tossing game (cyber ball) inducing negative emotions, and an adapted version of the virtual penalty kicking game. Throughout cyber ball, participants were included or ostracized by two other players in different experimental blocks. Participants were instructed to explicitly show, not regulate, or hide their emotions in different experimental blocks. Results provided some evidence for deficient processing of positive emotions in ADHD. Patients reported slightly lower positive affect than controls during cyber ball, gave lower valence ratings than controls in response to pleasant penalty kicking trials, and showed lower zygomaticus activations than controls especially during penalty kicking. Patients in comparison with controls showed slightly increased processing of unpleasant events during cyber ball (higher ratings of negative affect, especially in response to ostracism), but not during penalty kicking. Patients showed lower baseline skin conductance levels than controls, and impaired skin conductance modulations. Compared to controls, patients showed slight over-expression of positive as well as negative emotional behavior. Emotion regulation analyses revealed no major difficulties of ADHD vs. controls in altering their emotional reactions through deliberate response modulation. Moreover, patients reported to habitually apply adaptive emotion regulation strategies even more frequently than controls. The analyses of genetic high-risk vs. low-risk groups for ADHD across the whole sample revealed similar results as analyses for patients vs. controls for zygomaticus modulations during emotion processing, and for modulations of emotional reactions due to emotion regulation.
To sum up, the virtual penalty kicking paradigm proved to be successful for the induction of positive, but not negative emotions. The importance of presence in virtual reality for the intensity of induced emotions could be replicated. ADHD patients showed impaired processing of primarily positive emotions. Aberrations in negative emotional responding were less clear and need further investigation. Results point to adult ADHD in comparison to healthy controls suffering from baseline deficits in autonomic arousal and deficits in arousal modulation. Deficits of ADHD in the deliberate application of response-focused emotion regulation could not be found.
11 Conclusion
11.1 Glaze compositions
Glazes from tiles of imposing Islamic buildings and some tableware glazes of the medieval epoch in Central Asia, the Middle East, Asia Minor, and North Africa are analysed regarding their main composition and colouring agents. Three major production recipes can be distinguished, i.e. alkali glazes, alkali lead glazes, and lead glazes. In the work of Tite (2011), Islamic glazes from Egypt, Iran, Iraq, and Syria are subdivided into four groups of composition, being partly consistent with those of this work. The alkali lime glazes with <2 wt% PbO correspond to the alkali glazes, but with higher content of CaO. The second and third group of low lead alkali and lead alkali glazes (2-10 wt% PbO and 10-35 wt% PbO) can be subsumed to the alkali lead group described here. Tite´s high lead group has PbO contents >35 wt% and is comparable to the lead glazes (>30 wt% PbO) of this study. The lead and the alkali oxides serve as a flux for the lowering the melting point.
In the interaction of ceramic body and glaze, primarily an influence from Si, Al, and K is observed in the line scans from the cross section of ceramic and glaze. However, the input of ceramic material doesn’t seem to be critical for the classification of glazes according to their alkali and alkali lead compositions.
In every epoch and locality, except of the Ilkhanate dynasty in Iran, lead glaze samples can be verified. This is also observed in previous investigations e.g. from medieval Iraq, Jordan and Iran (McCarthy, 1996; Al-Saad, 2002; Holakooei et al., 2014). In the Moroccan and Bulgarian glazes, lead seems to be the only important flux. In part, the lead flux is supplemented by additional alkali contents. The lack of alkali and alkali lead glazes in Bulgarian and Moroccan glazes (assuming that the Ottoman alkali lead glazes are imported tableware) seems to affect the regions with Roman-influenced history and with geographical distance to the Near East alkali flux tradition.
For the alkali lead glazes and alkali glazes, the overall characteristic is sodium dominated, although the absolute soda values are in part surprisingly low. Samples from Bukhara, Takht-i-Suleiman and the Turkish localities have the highest, but still moderate Na2O values up to 15 wt%, compared to other analyses from e.g. India (Gill & Rehren, 2011).
The source of the alkali flux is either mineral natron or plant ash. The source can be determined regarding the MgO values, limited to 1.3 wt% in mineral natron and exceeding 2.0 wt% in the case of plant ashes. In the samples of the present study, the K2O component is not suitable for the indication of the flux-relevant alkali source due to its broad scattering. The P2O5 contents are also enhanced in the plant ash compositions but the data set is not sufficient for statistical evaluation. An influence of the ceramic body on the glaze composition is observed only for SiO2, Al2O3, and K2O in quartz frit ceramics with slight K-feldspar content.
The earliest Uzbek tableware glazes from the 10th-11th century (Seljuq period) were generally produced using a lead flux. The same applies to part of the Uzbek tile glazes which were produced between the 13th and 16th century. In Iran, glazes from the 12th century (Khwarezmid period) are lead glazes, but also alkali-fluxed glazes with mineral natron characteristics can be found. Although the production of lead-rich glazes was established from the 8th-9th century on in Iraq, Syria, and Egypt (Henshaw, 2010; Tite et al., 2011), alkali glazes are found in almost all regions except of Bulgaria and Morocco.
Plant ash-fluxed alkali glazes are found in 13th century glazes from Takht-i-Suleiman. The plant ash flux technology is assumed to be continuously used in Mesopotamia, Iran, and Central Asia (Sayre & Smith, 1974; Henderson, 2009), but it could be shown that a parallel use of mineral natron parallel existed in the alkali glaze production from the 12th-15th century from Uzbekistan to Afghanistan. Mineral natron characteristics are also reported by Mason (2004) for Syrian and Iranian alkali glazes on lustre ware of the 8th-14th century. Tile glazes with partly mineral natron compositions are found in the Mughal architectural glazes from the 14th- 17th century from India (Gill et al., 2014).
Alkali and alkali lead tile glazes from Samarkand from the 13th century (Mongolian period) have mineral natron flux characteristics, but samples from the 15th century (Timurid period) show plant ash signature. Alkali fluxed Uzbek glazes from Bukhara from the 16th century (Sheibanid dynasty) are also made by plant ash flux and are subdivided into two groups with high and low sodium oxide content. The Afghan alkali glazes have sodium oxide contents similar to the sodium-poor Uzbek subgroup, which points to a possible exchange of glaze makers or glaze making technology from Uzbekistan and Afghanistan in the 15th-17th century. Regarding the extensive exchange of Timurid craftsmen in Central Asia, this option seems to be even more likely (Golombek, 1996). One sample from the 15th century from Afghanistan with mineral natron reveals that this material was parallel used in these centuries.
Concerning the colouring of the glazes, it has to be distinguished between pigments and colouring ions which are incorporated in the glassy matrix. The colouring agents for translucent glazes are cations of various transition metals. As ions, Co2+ (blue), Cu2+ (green in a lead rich matrix), Fe3+ (brown/black), Mn4+ (brown/black) and Mn3+ (violet) are determined by EPMA. For opaque yellow, white, and turquoise glazes, different pigments were used. The crystalline pigments are investigated by a µ XRD2 device with the result of SnO2, SiO2, and PbSiO4 as whitening agents. PbSiO4 and Pb2Sn2O6 are found in the yellow glaze, from which only the lead tin oxide causes the yellow colour. In the black glazes, different Cr-rich pigments, Cu-Cr-Mn-oxides and iron containing clinopyroxenes are found, even in samples of the same period and region. Cr-rich particles are also detected in two turquoise Afghan glazes from the 15th and 16th century. The use of the ions of Fe, Cu, Co, Cr, and Mn seems to be widely common in the Islamic glazes and corresponds to the described colouring agents in e.g. the study of Tite (2011). The use of opacifying SnO2 particles is widespread as it is reported from different Islamic glazes from Iraq, Iran, Egypt, and Syria (Henshaw, 2010; O´Kane, 2011; Tite, 2011). The colouring agents are known already from former, e.g. Egyptian, Roman and pre-islamic periods, but especially SnO2 pigments became increasingly widespread in the Islamic glazing tradition. The use of yellow and black pigments instead varies already within the buildings from Bukhara from Cr crystals and clino-pyroxenes in the mosque Khoja Zainuddin to a Cu-Cr-Mn-oxide in the madrassa Mir-i Arab of the same epoch.
Regarding the matrix compositions connected with the colouring, a certain assignment within the different locations and epochs can be seen. It is noticeable that e.g. the content of lead in turquoise glazes in Uzbekistan is in the range of 0.0-9.2 wt% Pb, whereas blue glazes are mostly alkali ones with PbO contents <2.0 wt%. The turquoise glazes show, that this restriction is not influenced by any defaults of availability and processability. The assumption of common addition of lead and tin to the glaze, which is already described for Iranian glazes of the 13th century (Allan et al., 1973) cannot be confirmed by correlations of tin and lead oxide in the compositions.
11.2 Portable XRF measurement
With the p-XRF, semi-quantitative information about the major element compositions is generated. The depth of the detectable signals depends on the analysed sample setup. The p-XRF data are collected with the XL3 Hybrid device of the company Analyticon Instruments. In the comparison of p-XRF results of the “mining” program from Uzbek glazes with EPMA results, the same major composition groups can be distinguished. The Moroccan glazes, all lead rich, are measured with the “mining” as well as with the “soil” program, revealing a better performance in the “mining” measurements. The deviations are nevertheless high, because of the high lead contents, which make the calculation of matrix correction difficult.
The measurement of the colouring oxides MnO2, CoO, and CuO is satisfying with the internal calibration of the device and even improved with the “mining” program measurement, if compared to the results of the “soil” program. The measurements of glaze imitations lead to better results than that of bulk glass. This can be attributed to the smoother surface texture.
In spite of the accuracy limits in the measurements of particular elements in glazes, the classification of flux composition into three groups could be confirmed with the p XRF analysis. The measurement precision is therefore sufficient for the semi-quantitative analysis of the flux characteristic of glazes. Especially for the on-site measurement of large sample quantities on historical buildings, the device is a suitable tool.
11.3 Restoration material
The ORMOCER® fulfils the requirements of stability, reversibility, and transparency, which are imposed to a modern restoration material. As pigments, historically coloured glass, cobalt blue, Egyptian blue, lead tin yellow, manganese violet, iron oxide, copper oxide, and cassiterite were used. The metal compounds have higher colour intensities than the pigments of coloured glass. It has to be considered that the proportion of ORMOCER® in the batch must be high enough (70 vol%) to guarantee the ORMOCER® properties of weathering and mechanical stability. The adhesion properties of the ORMOCER® and the homogeneity of the mixture are the best in a fraction of max. 30 vol% particles per ORMOCER®.
With integrated particles, the ORMOCER® G materials show homogeneous coatings, whereas the particles in the ORMCOER® E show more agglomeration. In the sedimentation and weathering experiments, the use of an ultrasonic finger in combination with a roller mill is favourable compared to the treatment with bead grinding mill. The treatments with ultrasonic finger and roller mill result in less sedimentation and better adhesion of the dispersions. The treatment of the dispersions in the bead grinding mill does not result in sufficient adhesion, certainly due to the sedimentation behaviour and a congregation of particles on the bottom of the coating.
The modification of dispersed nano-particles by 3-methacryl-oxypropyltrimethoxysilan leads to a further homogenization in the sedimentation tests. It is therefore approved for the use in coloured glaze supplements. In weathered coatings of nano-particle compounds, the surface modification shows certainly no enhancement of stability.
The treatment of pigmented coatings with an additional layer of pure ORMOCER® results in a bright and transparent appearing, which is closer to the original optical appearance of the glaze. A long-time test application on a historical building will be the next step to validate the suitability of the restoration material.
Graphs are a frequently used tool to model relationships among entities. A graph is a binary relation between objects, that is, it consists of a set of objects (vertices) and a set of pairs of objects (edges).
Networks are common examples of modeling data as a graph. For example, relationships between persons in a social network, or network links between computers in a telecommunication network can be represented by a graph.
The clearest way to illustrate the modeled data is to visualize the graphs. The field of Graph Drawing deals with the problem of finding algorithms to automatically generate graph visualizations. The task is to find a "good" drawing, which can be measured by different criteria such as number of crossings between edges or the used area. In this thesis, we study Angular Schematization in Graph Drawing. By this, we mean drawings
with large angles (for example, between the edges at common vertices or at crossing points).
The thesis consists of three parts. First, we deal with the placement of boxes. Boxes are axis-parallel rectangles that can, for example, contain text.
They can be placed on a map to label important sites, or can be used to describe semantic relationships between words in a word network. In the second part of the thesis, we consider graph drawings visually guide the
viewer. These drawings generally induce large angles between edges that meet at a vertex. Furthermore, the edges are drawn crossing-free and in a way that
makes them easy to follow for the human eye. The third and final part is devoted to crossings with large angles. In drawings with crossings, it is important to have large angles between edges at their crossing point, preferably right angles.
The present thesis considers the development and analysis of arbitrary Lagrangian-Eulerian
discontinuous Galerkin (ALE-DG) methods with time-dependent approximation spaces for
conservation laws and the Hamilton-Jacobi equations.
Fundamentals about conservation laws, Hamilton-Jacobi equations and discontinuous Galerkin
methods are presented. In particular, issues in the development of discontinuous Galerkin (DG)
methods for the Hamilton-Jacobi equations are discussed.
The development of the ALE-DG methods based on the assumption that the distribution of
the grid points is explicitly given for an upcoming time level. This assumption allows to construct a time-dependent local affine linear mapping to a reference cell and a time-dependent
finite element test function space. In addition, a version of Reynolds’ transport theorem can be
proven.
For the fully-discrete ALE-DG method for nonlinear scalar conservation laws the geometric
conservation law and a local maximum principle are proven. Furthermore, conditions for slope
limiters are stated. These conditions ensure the total variation stability of the method. In addition, entropy stability is discussed. For the corresponding semi-discrete ALE-DG method,
error estimates are proven. If a piecewise $\mathcal{P}^{k}$ polynomial approximation space is used on the reference cell, the sub-optimal $\left(k+\frac{1}{2}\right)$ convergence for monotone fuxes and the optimal $(k+1)$ convergence for an upwind flux are proven in the $\mathrm{L}^{2}$-norm. The capability of the method is shown by numerical examples for nonlinear conservation laws.
Likewise, for the semi-discrete ALE-DG method for nonlinear Hamilton-Jacobi equations, error
estimates are proven. In the one dimensional case the optimal $\left(k+1\right)$ convergence and in the two dimensional case the sub-optimal $\left(k+\frac{1}{2}\right)$ convergence are proven in the $\mathrm{L}^{2}$-norm, if a piecewise $\mathcal{P}^{k}$ polynomial approximation space is used on the reference cell. For the fullydiscrete method, the geometric conservation is proven and for the piecewise constant forward Euler step the convergence of the method to the unique physical relevant solution is discussed.
In order to select the appropriate behavior, it is important to choose the right behavior at the right time out of many options. It still remains unclear nowadays how exactly this is managed. To address this question, I expose flies (Drosophila melanogaster) to uncontrollable stress to study their behavior under restrictive circumstances by using the so-called shock box. Exposing animals to uncontrollable stress may have an impact on subsequent behavior and can last for some time. The animal learns that whatever it does, it cannot change the situation and therefore can develop something called learned helplessness. The term was first conceptualized by two American psychologists Maier and Seligman (1967), who discovered this phenomenon while doing experiments with dogs. They found out that dogs which are exposed to inescapable stress, later fail in a learning task (‘shuttle box’).
In this work the walking patterns of three different types of experimental flies, walking in a small dark chamber, were evaluated. Using the triadic design (Seligman and Maier, 1967), flies were either exposed to electric shock randomly (yoked), could turn it off by being active (master) or did not receive punishment at all (control). Master flies were shocked whenever they sat for more than 0.9 seconds. At the same time yoked flies received a shock as well independent of what they were doing, to ensure the same amount of shocks received and to create random punishment pattern for the yoked group. With this so-called no-idleness paradigm flies were conditioned either 10 minutes, which resulted in a short (3 minutes) after-effect, or 20 minutes that turned out to be more stable (10 minutes).
In a second part, the behavior during the 20 minute conditioning and a 10 minutes post-test was described in detail. Female flies of the yoked group developed lower activity levels, longer pauses and walked more slowly than master and control flies during conditioning. In the time after the shocks while still in the box, the yoked flies also reduced the frequency and duration of walking bouts as well as their walking speed. Additionally, they took more time to resume walking after the onset of an electric shock than master flies (escape latency) and turned out to make less pauses lasting between 1-1.5 seconds which supports the finding concerning the escape latency.
Male flies, tested under the same conditions, showed a slightly weaker after-effect regarding the difference between master and yoked during conditioning and post-test when compared to female flies.
When comparing the 20 minutes conditioning with subsequent 10 minutes test in the heat and the shock box in parallel, one finds the same effect: Flies which do not have control over the shocks, lower their activity, make less but longer pauses and walk more slowly than their respective master flies. Despite the similar effect of heat and shock on the flies, some differences between the devices occurred, which can partly be explained by different humidity conditions as well as by different surfaces within the chambers.
When the control over the shocks is given back to the yoked flies, it takes them about seven minutes to realize it. One could also show that dopamine levels in the brain were reduced in comparison to flies which did not receive shocks. Yoked flies also were impaired in a place learning task (place learning) and their reaction to light (exit from the box towards the light) directly after conditioning.
After characterizing the walking behavior in the chambers, the study deals with the question whether the effects observed in the chambers transfer to different environments.
In free walk they only differed from flies which did not receive electric shocks and no effect of uncontrollability was transferred to courtship behavior. Handling as the cause could be excluded. Since handling could be exclude to be the cause of losing the effect, I assumed that the behavior shown in the boxes are context depend.
Not only were the after-effects of inescapable shock subject of the current research also the impact of the rearing situation on the response to electric shock was investigated in the present study. Flies which grew up in a single-reared situation turned out to be less affected by inescapable stress in both sexes.
In the next part, the first steps to unravel the neuronal underpinning were taken. A mutant – fumin – which is defective in the dopamine re-uptake transporter showed less reaction to inescapable foot shocks, while a mutant for the gene which encodes an adenylate cyclase (rutabaga2080) resulted in a good score during conditioning, but showed no stable after-effect. Downregulating the expression of the adenylate cyclase gene (rutabaga) in different parts of the mushroom bodies showed, that rutabaga is necessary in the α’β’-lobes for expressing the differences between master and yoked flies in the no-idleness paradigm. The study further confirmed previous findings, that rutabaga is needed in operant but not in classical conditioning.
As a result, the study could show that not the stimulus itself causes the state of uncontrollability but the fact that the fly learned that it was not in control of the stimulus. This state turned out to be context and time dependent.
Beyond the state of the art, towards intuitive and reliable non-visual Brain-Computer-Interfacing
(2016)
For the present work three main goals were formulated:
goal 1 To design a tactile BCI used for mobility which is
intuitive (G1.1), reliable and fast while being usable
by participants aged 50 years and above.
goal 2 To design an auditory BCI used for communication
which is intuitive and reliable.
goal 3 To examine the effects of training on tactile and
auditory BCI performance.
Three studies were performed to achieve these goals.
In the first study nine participants aged above 50 years
performed a five-session training after which eight participants
were able to navigate a virtual wheelchair with
mean accuracy above 95% and an ITR above 20 bits / min.
In the second study 15 participants, four of them endusers
with motor-impairment, were able to communicate
meaningful with high accuracies using an auditory BCI.
In the third study nine healthy and nine visually impaired
participants (regarded as sensory experts for non-visual
perception) performed tactile, auditory and visual (for
healthy participants only) copy tasks. Participants with
trained perception significantly outperformed control
participants for tactile but not for auditory performance.
Tactile performance of sensory experts was on equal levels
as the visual performance of control participants.
We were able to demonstrate viability of intuitive gazeindependent
tactile and auditory BCI. Our tactile BCI performed
on levels similar to those of visual BCI, outperforming
current tactile BCI protocols. Furthermore, we were
able to demonstrate significant beneficial effect of training
on tactile BCI performance. Our results demonstrate previously
untapped potential for tactile BCI and avenues for
future research in the field of gaze-independent BCI.
Biochemical and molecular characterization of an original master sex determining gene in Salmonids
(2016)
Sexual development is a fundamental and versatile process that shapes animal morphology, physiology and behavior. The underlying developmental process is composed of the sex determination and the sex differentiation. Sex determination mechanisms are extremely labile among taxa. The initial triggers of the sex determination process are often genetics called sex determining genes. These genes are expressed in the bipotential gonad and tilt the balance to a developmental program allowing the differentiation of either a testis or an ovary. Fish represent a large and fascinating vertebrate group to study both sex determination and sex differentiation mechanisms. To date, among the known sex determining genes, three gene families namely sox, dmrt and TGF-β factors govern this developmental program. As exception to this rule, sdY “sexually dimorphic on the Y” does not belong to one of these families as it comes from the duplication / evolution of an ancestor gene related to immunity, i.e., the interferon related factor 9, irf9. sdY is the master sex determining gene in salmonids, a group of fishes that include species such as rainbow trout and Atlantic salmon. The present study was aimed to firstly characterize the features of SdY protein. Results indicate that SdY is predominantly localized in the cytoplasm tested in various fish and mammalian cell lines and confirmed by different methods. Predictive in silico analysis revealed that SdY is composed of a β-sandwich core surrounded by three α-helices as well specific characteristics conferring a putative protein-protein interaction site. Secondly, the study was aimed to understand how SdY could trigger testicular differentiation. SdY is a truncated divergent version of Irf9 that has a conserved protein-protein domain but lost the DNA interaction domain of its ancestor gene. It was then hypothesized that SdY could initiate testicular differentiation by protein-protein interactions. To evaluate this we first conducted a yeast-two-hybrid screen that revealed a high proportion of transcription factors including fox proteins. Using various biochemical and cellular methods we confirm an interaction between SdY and Foxl2, a major transcription factor involved in ovarian differentiation and identity maintenance. Interestingly, the interaction of SdY with Foxl2 leads to nuclear translocation of SdY from the cytoplasm. Furthermore, this SdY translocation mechanism was found to be specific to fish Foxl2 and to a lesser extend Foxl3 and not other Fox proteins or mammalian FoxL2. In addition, we found that this interaction allows the stabilization of SdY and prevents its degradation. Finally, to better decipher SdY action we used as a model a mutated version of SdY that was identified in XY females of Chinook salmon natural population. Results show that this mutation induces a local conformation defect obviously leading to a misfolded protein and a quick degradation. Moreover, the mutated version compromised the interaction with Foxl2 defining a minimal threshold to induce testicular differentiation. Altogether results from my thesis propose that SdY would trigger testicular differentiation in salmonids by preventing Foxl2 to promote ovarian differentiation. Further research should be now carried out on how this interaction of SdY and Foxl2 acts in-vivo.