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- Theodor-Boveri-Institut für Biowissenschaften (67)
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Sonstige beteiligte Institutionen
The idea that our observable Universe may have originated from a quantum tunneling event out of an eternally inflating false vacuum state is a cornerstone of the multiverse paradigm. Modern theories that are considered as an approach towards the ultraviolet-complete fundamental theory of particles and gravity, such as the various types of string theory, even suggest that a vast landscape of different vacuum configurations exists, and that gravitational tunneling is an important mechanism with which the Universe can explore this landscape. The tunneling scenario also presents a unique framework to address the initial conditions of our observable Universe. In particular, it allows to introduce deviations from the cosmological concordance model in a controlled and well-motivated way. These deviations are a central topic of this work. An important feature in most of the theories mentioned above is the presumed existence of additional space dimensions in excess of the three which we observe in our every-day experience. It was realized that these extra dimensions could avoid our detection if they are compactified to microscopic length scales far beyond the reach of current experiments. There also seem to be natural mechanisms available for dynamical compactification in those theories. These typically lead to a vast landscape of different vacuum configurations which also may differ in the number of macroscopic dimensions, only the total number of dimensions being determined by the theory. Transitions between these vacuum configurations may hence open up new directions which were previously compact, spontaneously compactify some previously macroscopic directions, or otherwise re-arrange the configuration of compact and macroscopic dimensions in a more general way. From within the bubble Universe, such a process may be perceived as an anisotropic background spacetime - intuitively, the dimensions which open up may give rise to preferred directions. If our 3+1 dimensional observable Universe was born in a process as described above, one may expect to find traces of a preferred direction in cosmological observations. For instance, two directions could be curved like on a sphere, while the third space direction is flat. Using a scenario of gravitational tunneling to fix the initial conditions, I show how the primordial signatures in such an anisotropic Universe can be obtained in principle and work out a particular example in more detail. A small deviation from isotropy also has phenomenological consequences for the later evolution of the Universe. I discuss the most important effects and show that backreaction can be dynamically important. In particular, under certain conditions, a buildup of anisotropic stress in different components of the cosmic fluid can lead to a dynamical isotropization of the total stress-energy tensor. The mechanism is again demonstrated with the help of a physical example.
Background: Gene function analysis of the obligate intracellular bacterium Chlamydia pneumoniae is hampered by the facts that this organism is inaccessible to genetic manipulations and not cultivable outside the host. The genomes of several strains have been sequenced; however, very little information is available on the gene structure and transcriptome of C. pneumoniae. Results: Using a differential RNA-sequencing approach with specific enrichment of primary transcripts, we defined the transcriptome of purified elementary bodies and reticulate bodies of C. pneumoniae strain CWL-029; 565 transcriptional start sites of annotated genes and novel transcripts were mapped. Analysis of adjacent genes for cotranscription revealed 246 polycistronic transcripts. In total, a distinct transcription start site or an affiliation to an operon could be assigned to 862 out of 1,074 annotated protein coding genes. Semi-quantitative analysis of mapped cDNA reads revealed significant differences for 288 genes in the RNA levels of genes isolated from elementary bodies and reticulate bodies. We have identified and in part confirmed 75 novel putative non-coding RNAs. The detailed map of transcription start sites at single nucleotide resolution allowed for the first time a comprehensive and saturating analysis of promoter consensus sequences in Chlamydia. Conclusions: The precise transcriptional landscape as a complement to the genome sequence will provide new insights into the organization, control and function of genes. Novel non-coding RNAs and identified common promoter motifs will help to understand gene regulation of this important human pathogen.
Background:
Competing risks methodology allows for an event-specific analysis of the single components of composite time-to-event endpoints. A key feature of competing risks is that there are as many hazards as there are competing risks. This is not always well accounted for in the applied literature.
Methods:
We advocate a simulation point of view for understanding competing risks. The hazards are envisaged as momentary event forces. They jointly determine the event time. Their relative magnitude determines the event type. 'Empirical simulations' using data from a recent study on cardiovascular events in diabetes patients illustrate subsequent interpretation. The method avoids concerns on identifiability and plausibility known from the latent failure time approach.
Results:
The 'empirical simulations' served as a proof of concept. Additionally manipulating baseline hazards and treatment effects illustrated both scenarios that require greater care for interpretation and how the simulation point of view aids the interpretation. The simulation algorithm applied to real data also provides for a general tool for study planning.
Conclusions:
There are as many hazards as there are competing risks. All of them should be analysed. This includes estimation of baseline hazards. Study planning must equally account for these aspects.
The work presented in this thesis was mainly targeted at exploring the capabilities of evaporation based LC detectors as well as further alternatives for the control of impurities in substances not exhibiting a suitable chromophore for UV-detection. In the course of the work carried out, several new methods for the identification, impurities control and composition testing of APIs were elaborated. An evaporation based detector that entered into the field of pharmaceutical analysis in the recent years was the Evaporative Light Scattering Detector (ELSD). However, non-reproducible spikes were reported when injecting concentrated test solutions as they are usually required for the control of impurities. The reasons, for the appearance of these spikes as well as possibilities for their avoidance were explored in a systematic study. Moreover, the dependence of the detector sensitivity on different eluent composition, eluent flow-rate and ELSD settings was investigated. In the course of the revision of the Ph.Eur. monographs for aspartic acid and alanine, a C18 reversed phase ion-pair LC method using 1 mmol/L of perfluoroheptanoic acid as an ion-pair reagent and a charged aerosol detector (CAD) was developed and fully validated for the purity control of Asp. The method was capable of separating the organic acids and major amino acids known to occur as process related impurities. With a slight modification, the method was also applicable for the purity control of Ala. Based on the developed LC-CAD method for the impurity control of alanine, a comparative study of the performance characteristics of different evaporation based LC detectors, i.e. ELSD, CAD and the recently developed Nano Quantity Analyte Detector (NQAD) was carried out. Additionally, an MS detector and qNMR were included in this study. It was found that the control of impurities in Alanine at an ICH conform level could be ensured using LC coupled to CAD, MSD and NQAD detection as well as by the use of qNMR. In terms of performance, prize and ease of use CAD and NQAD were found to be the most suitable alternatives. In terms of repeatability and sensitivity, the CAD appeared slightly superior to the NQAD. The quality of streptomycin sulfate is not sufficiently controlled by the current Ph.Eur. monograph in that an appropriate test for the control of the related substances is missing. A study was carried out to develop a C18 reversed phase ion-pair LC method using pentafluoropropionic acid as an ion-pair reagent and a CAD for the identification and control of the related substances. The developed method allowed the separation of 21 impurities from streptomycin. Moreover, coupling of the method to MS allowed the identification of the separated impurities. The method was shown to be sufficiently sensitive to control the related substances with a disregard limit of 0.1% as it is normally applied in the Ph.Eur. for products derived from fermentation. Currently, the aescin content of horse-chestnut standardized dry extract is determined using a complex and laborious photometric determination. A more selective LC-UV assay determination for beta-aescin has been proposed for the Ph.Eur. draft monograph of horse-chestnut standardized dry extract. Possibilities were explored to further improve the LC-method using detection by CAD. It was demonstrated that by the use of a modified LC-CAD method several problems related to the differences in the UV-response of the various components contained in the active aescin fraction could be eliminated. Moreover the proposed reference standard strategy was reviewed. Eventually, it was demonstrated on the example of two different clusters of pharmacologically active peptides how low energy collision induced dissociation mass spectrometry (low energy CID-MS) can successfully be used for identification testing in pharmacopoeial monographs. In this respect, the combination of a direct confirmation of the molecular mass via the m/z-ratio of the molecule ions with structural sequence information obtained by low energy CID-MS experiments was found to deliver a higher degree of certainty of the identity of a given substance than the set of tests currently described in the monographs. A significant gain in efficiency and throughput and important reduction of the amount of sample consumed during testing were identified as being additional advantages of this approach. Taken together, it could be demonstrated on various examples how recent technological advancements in the field of analytical chemistry can contribute to improve the quality control of APIs.
It has been proposed that different features of a face provide a source of information for separate perceptual and cognitive processes. Properties of a face that remain rather stable over time, so called invariant facial features, yield information about a face’s identity, and changeable aspects of faces transmit information underlying social communication such as emotional expressions and speech movements. While processing of these different face properties was initially claimed to be independent, a growing body of evidence suggests that these sources of information can interact when people recognize faces with whom they are familiar. This is the case because the way a face moves can contain patterns that are characteristic for that specific person, so called idiosyncratic movements. As a face becomes familiar these idiosyncratic movements are learned and hence also provide information serving face identification. While an abundance of experiments has addressed the independence of invariant and variable facial features in face recognition, little is known about the exact nature of the impact idiosyncratic facial movements have on face recognition. Gaining knowledge about the way facial motion contributes to face recognition is, however, important for a deeper understanding of the way the brain processes and recognizes faces. In the following dissertation three experiments are reported that investigate the impact familiarity of changeable facial features has on processes of face recognition. Temporal aspects of the processing of familiar idiosyncratic facial motion were addressed in the first experiment via EEG by investigating the influence familiar facial movement exerts on event-related potentials associated to face processing and face recognition. After being familiarized with a face and its idiosyncratic movement, participants viewed familiar or unfamiliar faces with familiar or unfamiliar facial movement while their brain potentials were recorded. Results showed that familiarity of facial motion influenced later event-related potentials linked to memory processes involved in face recognition. The second experiment used fMRI to investigate the brain areas involved in processing familiar facial movement. Participants’ BOLD-signal was registered while they viewed familiar and unfamiliar faces with familiar or unfamiliar idiosyncratic movement. It was found that activity of brain regions, such as the fusiform gyrus, that underlie the processing of face identity, was modulated by familiar facial movement. Together these two experiments provide valuable information about the nature of the involvement of idiosyncratic facial movement in face recognition and have important implications for cognitive and neural models of face perception and recognition. The third experiment addressed the question whether idiosyncratic facial movement could increase individuation in perceiving faces from a different ethnic group and hence reduce impaired recognition of these other-race faces compared to own-race faces, a phenomenon named the own-race bias. European participants viewed European and African faces that were each animated with an idiosyncratic smile while their attention was either directed to the form or the motion of the face. Subsequently recognition memory for these faces was tested. Results showed that the own-race bias was equally present in both attention conditions indicating that idiosyncratic facial movement was not able to reduce or diminish the own-race bias. In combination the here presented experiments provide further insight into the involvement of idiosyncratic facial motion in face recognition. It is necessary to consider the dynamic component of faces when investigating face recognition because static facial images are not able to provide the full range of information that leads to recognition of a face. In order to reflect the full process of face recognition, cognitive and neural models of face perception and recognition need to integrate dynamic facial features as a source of information which contributes to the recognition of a face.
While beneficial sponge-microbe associations have received much attention in recent years, less effort has been undertaken to investigate the interactions of sponges with potentially pathogenic microorganisms. Thus, the aim of this study was to examine two selected Caribbean disease conditions, termed “Sponge Orange Band” and “Sponge White Patch”, via ecological and molecular methods. Sponge Orange Band (SOB) disease affects the prominent Caribbean barrel sponge Xestospongia muta that is counted among the high-microbial-abundance (HMA) sponges, whereas Sponge White Patch (SWP) disease affects the abundant rope sponge Amphimedon compressa that belongs to the low-microbial-abundance (LMA) sponges. I have documented for both Caribbean sponge diseases a disease progression going along with massive tissue destruction as well as loss of the characteristic microbial signatures. Even though new bacteria were shown to colonize the bleached areas, the infection trials revealed in both cases no indication for the involvement of a microbial pathogen as an etiologic agent of disease leaving us still in the dark about the cause of Sponge Orange Band as well as Sponge White Patch disease.
Background:
The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest.
Results:
We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families.
Conclusions:
This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.
Context:
Adrenal tumors have a prevalence of around 2% in the general population. Adrenocortical carcinoma (ACC) is rare but accounts for 2–11% of incidentally discovered adrenal masses. Differentiating ACC from adrenocortical adenoma (ACA) represents a diagnostic challenge in patients with adrenal incidentalomas, with tumor size, imaging, and even histology all providing unsatisfactory predictive values.
Objective:
Here we developed a novel steroid metabolomic approach, mass spectrometry-based steroid profiling followed by machine learning analysis, and examined its diagnostic value for the detection of adrenal malignancy.
Design:
Quantification of 32 distinct adrenal derived steroids was carried out by gas chromatography/mass spectrometry in 24-h urine samples from 102 ACA patients (age range 19–84 yr) and 45 ACC patients (20–80 yr). Underlying diagnosis was ascertained by histology and metastasis in ACC and by clinical follow-up [median duration 52 (range 26–201) months] without evidence of metastasis in ACA. Steroid excretion data were subjected to generalized matrix learning vector quantization (GMLVQ) to identify the most discriminative steroids.
Results:
Steroid profiling revealed a pattern of predominantly immature, early-stage steroidogenesis in ACC. GMLVQ analysis identified a subset of nine steroids that performed best in differentiating ACA from ACC. Receiver-operating characteristics analysis of GMLVQ results demonstrated sensitivity = specificity = 90% (area under the curve = 0.97) employing all 32 steroids and sensitivity = specificity = 88% (area under the curve = 0.96) when using only the nine most differentiating markers.
Conclusions:
Urine steroid metabolomics is a novel, highly sensitive, and specific biomarker tool for discriminating benign from malignant adrenal tumors, with obvious promise for the diagnostic work-up of patients with adrenal incidentalomas.
The title compound, [Zr(3)(C(14)H(20)Si(2))(3)O(3)], consists of three disila-bridged zirconocene units, which are connected via an oxide ligand, forming a nearly planar six-membered ring with a maximum displacement of 0.0191 (8) A. The compound was isolated as a by-product from a mixture of [(C(5)H(4)SiMe(2))(2)ZrCl(2)] and Li[AlH(4)] in Et(2)O.
Background:
Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. We previously described GLV-1h68, a modified Vaccinia Virus with exclusive tropism for tumor cells, and we observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro and its ability to colonize and eliminate tumor in vivo.
Methods:
In the current study we surveyed the in vitro permissivity to GLV-1h68 replication of the NCI-60 panel of cell lines. Selected cell lines were also tested for permissivity to another Vaccinia Virus and a vesicular stomatitis virus (VSV) strain. In order to identify correlates of permissity to viral infection, we measured transcriptional profiles of the cell lines prior infection.
Results:
We observed highly heterogeneous permissivity to VACV infection amongst the cell lines. The heterogeneity of permissivity was independent of tissue with the exception of B cell derivation. Cell lines were also tested for permissivity to another Vaccinia Virus and a vesicular stomatitis virus (VSV) strain and a significant correlation was found suggesting a common permissive phenotype. While no clear transcriptional pattern could be identified as predictor of permissivity to infection, some associations were observed suggesting multifactorial basis permissivity to viral infection.
Conclusions:
Our findings have implications for the design of oncolytic therapies for cancer and offer insights into the nature of permissivity of tumor cells to viral infection.