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The field of genetics faces a lot of challenges and opportunities in both research and diagnostics due to the rise of next generation sequencing (NGS), a technology that allows to sequence DNA increasingly fast and cheap.
NGS is not only used to analyze DNA, but also RNA, which is a very similar molecule also present in the cell, in both cases producing large amounts of data.
The big amount of data raises both infrastructure and usability problems, as powerful computing infrastructures are required and there are many manual steps in the data analysis which are complicated to execute.
Both of those problems limit the use of NGS in the clinic and research, by producing a bottleneck both computationally and in terms of manpower, as for many analyses geneticists lack the required computing skills.
Over the course of this thesis we investigated how computer science can help to improve this situation to reduce the complexity of this type of analysis.
We looked at how to make the analysis more accessible to increase the number of people that can perform OMICS data analysis (OMICS groups various genomics data-sources).
To approach this problem, we developed a graphical NGS data analysis pipeline aimed at a diagnostics environment while still being useful in research in close collaboration with the Human Genetics Department at the University of Würzburg.
The pipeline has been used in various research papers on covering subjects, including works with direct author participation in genomics, transcriptomics as well as epigenomics.
To further validate the graphical pipeline, a user survey was carried out which confirmed that it lowers the complexity of OMICS data analysis.
We also studied how the data analysis can be improved in terms of computing infrastructure by improving the performance of certain analysis steps.
We did this both in terms of speed improvements on a single computer (with notably variant calling being faster by up to 18 times), as well as with distributed computing to better use an existing infrastructure.
The improvements were integrated into the previously described graphical pipeline, which itself also was focused on low resource usage.
As a major contribution and to help with future development of parallel and distributed applications, for the usage in genetics or otherwise, we also looked at how to make it easier to develop such applications.
Based on the parallel object programming model (POP), we created a Java language extension called POP-Java, which allows for easy and transparent distribution of objects.
Through this development, we brought the POP model to the cloud, Hadoop clusters and present a new collaborative distributed computing model called FriendComputing.
The advances made in the different domains of this thesis have been published in various works specified in this document.
The paper argues that a) Germanic *tauf/ƀra- (Germ. Zauber, etc.) is related to a root PIE *deu̯p- ‘beat; make a hollow sound, resound’ found in Greek δοῦπος ‘thud’, etc., b) Greek φάρμακον goes back to the root PIE *gʷʰer- ‘heat’ (Gk. θερμός, etc.) implying healing by fomentation, and c) Armenian hiwand ‘sick’, borrowed from Iranian, to PIE *sh₂ei̯- ‘bind’ relying on the notion of disease as a supernatural bond.
Over recent years next generation sequencing (NGS) technologies evolved from costly tools used by very few, to a much more accessible and economically viable technology. Through this recently gained popularity, its use-cases expanded from research environments into clinical settings. But the technical know-how and infrastructure required to analyze the data remain an obstacle for a wider adoption of this technology, especially in smaller laboratories. We present GensearchNGS, a commercial DNAseq software suite distributed by Phenosystems SA. The focus of GensearchNGS is the optimal usage of already existing infrastructure, while keeping its use simple. This is achieved through the integration of existing tools in a comprehensive software environment, as well as custom algorithms developed with the restrictions of limited infrastructures in mind. This includes the possibility to connect multiple computers to speed up computing intensive parts of the analysis such as sequence alignments. We present a typical DNAseq workflow for NGS data analysis and the approach GensearchNGS takes to implement it. The presented workflow goes from raw data quality control to the final variant report. This includes features such as gene panels and the integration of online databases, like Ensembl for annotations or Cafe Variome for variant sharing.
Background: Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown.
Methods: Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163.
Results: 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway.
Conclusions: This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization.
Background: Regular exercise is beneficial for cardiovascular health but a recent meta-analysis indicated a relationship between extensive endurance sport and a higher risk of atrial fibrillation, an independent risk factor for stroke. However, data on the frequency of cardiac arrhythmias or (clinically silent) brain lesions during and after marathon running are missing.
Methods/Design: In the prospective observational "Berlin Beat of Running" study experienced endurance athletes underwent clinical examination (CE), 3 Tesla brain magnetic resonance imaging (MRI), carotid ultrasound imaging (CUI) and serial blood sampling (BS) within 2-3 days prior (CE, MRI, CUI, BS), directly after (CE, BS) and within 2 days after (CE, MRI, BS) the 38\(^{th}\) BMW BERLIN-MARATHON 2011. All participants wore a portable electrocardiogram (ECG)-recorder throughout the 4 to 5 days baseline study period. Participants with pathological MRI findings after the marathon, troponin elevations or detected cardiac arrhythmias will be asked to undergo cardiac MRI to rule out structural abnormalities. A follow-up is scheduled after one year.
Results: Here we report the baseline data of the enrolled 110 athletes aged 36-61 years. Their mean age was 48.8 \(\pm\) 6.0 years, 24.5% were female, 8.2% had hypertension and 2.7% had hyperlipidaemia. Participants have attended a mean of 7.5 \(\pm\) 6.6 marathon races within the last 5 years and a mean of 16 \(\pm\) 36 marathon races in total. Their weekly running distance prior to the 38\(^{th}\) BMW BERLIN-MARATHON was 65 \(\pm\) 17 km. Finally, 108 (98.2%) Berlin Beat-Study participants successfully completed the 38\(^{th}\) BMW BERLIN-MARATHON 2011.
Discussion: Findings from the "Berlin Beats of Running" study will help to balance the benefits and risks of extensive endurance sport. ECG-recording during the marathon might contribute to identify athletes at risk for cardiovascular events. MRI results will give new insights into the link between physical stress and brain damage.
LMNA-related dilated cardiomyopathy is an inherited heart disease caused by mutations in the LMNA gene encoding for lamin A/C. The disease is characterized by left ventricular enlargement and impaired systolic function associated with conduction defects and ventricular arrhythmias. We hypothesized that LMNA-mutated patients' induced Pluripotent Stem Cell-derived cardiomyocytes (iPSC-CMs) display electrophysiological abnormalities, thus constituting a suitable tool for deciphering the arrhythmogenic mechanisms of the disease, and possibly for developing novel therapeutic modalities. iPSC-CMs were generated from two related patients (father and son) carrying the same E342K mutation in the LMNA gene. Compared to control iPSC-CMs, LMNA-mutated iPSC-CMs exhibited the following electrophysiological abnormalities: (1) decreased spontaneous action potential beat rate and decreased pacemaker current (I\(_f\)) density; (2) prolonged action potential duration and increased L-type Ca\(^{2+}\) current (I\(_{Ca,L}\)) density; (3) delayed afterdepolarizations (DADs), arrhythmias and increased beat rate variability; (4) DADs, arrhythmias and cessation of spontaneous firing in response to β-adrenergic stimulation and rapid pacing. Additionally, compared to healthy control, LMNA-mutated iPSC-CMs displayed nuclear morphological irregularities and gene expression alterations. Notably, KB-R7943, a selective inhibitor of the reverse-mode of the Na\(^+\)/Ca\(^{2+}\) exchanger, blocked the DADs in LMNA-mutated iPSC-CMs. Our findings demonstrate cellular electrophysiological mechanisms underlying the arrhythmias in LMNA-related dilated cardiomyopathy.
Imbalancen im Bereich der autonomen Innervation des Herzens auf Sinusknotenebene zeigen sich anhand des Fehlens der „heart rate variability“ und der „heart rate turbulence“ und werden bereits zur Risikoeinschätzung von KHK-Patienten herangezogen, während Untersuchungen zur autonomen Dysbalance auf Ventrikelebene bisher kaum durchgeführt wurden. Daher war das Ziel dieser Arbeit eine Risikostratifizierung von Patienten nach einem Myokardinfarkt anhand dynamischer Veränderungen der QT-Zeit, zu denen es nach einer ventrikulären Extrasystole kommt. In der Einleitung wird die Wichtigkeit der Beachtung allgemeiner kardiovaskulärer Risikofaktoren erläutert. Es wird auf die Komplexität der QT-Zeit, deren beeinflussende Faktoren sowie auf den Einfluss des autonomen Nervensystems auf die Repolarisation der Herzkammern eingegangen. Im Abschnitt „Material und Methode“ und in „Auswertungen und Berechnungen“ wird das Patientenkollektiv vorgestellt, außerdem werden die Programme beschrieben, die zum Erzeugen der Daten verwendet wurden. Als Ergebnis lässt sich festhalten, dass Schlag-zu-Schlag-Analysen der QT-Zeit nach ventrikulären Extrasystolen signifikante Unterschiede aufzeigen zwischen den Patienten, die einen Follow-up von zwei Jahren nach einem Myokardinfarkt überlebt haben und denen, die während dieses Beobachtungszeitraumes aufgrund kardiovaskulärer Komplikationen verstarben. Der Aufwand, der hierfür betrieben werden muss, ist jedoch so hoch, dass diese Analysen wohl nicht zur routinemäßigen Anwendung kommen werden.
New techniques in molecular genetic diagnostics now allow for accurate diagnosis in a large proportion of patients with muscular diseases. Nevertheless, many patients remain unsolved, although the clinical history and/or the muscle biopsy give a clear indication of the involved genes. In many cases, there is a strong suspicion that the cause must lie in unexplored gene areas, such as deep-intronic or other non-coding regions. In order to find these changes, next-generation sequencing (NGS) methods are constantly evolving, making it possible to sequence entire genomes to reveal these previously uninvestigated regions. Here, we present a young woman who was strongly suspected of having a so far genetically unsolved sarcoglycanopathy based on her clinical history and muscle biopsy. Using short read whole genome sequencing (WGS), a homozygous inversion on chromosome 13 involving SGCG and LINC00621 was detected. The breakpoint in intron 2 of SGCG led to the absence of γ-sarcoglycan, resulting in the manifestation of autosomal recessive limb-girdle muscular dystrophy 5 (LGMDR5) in the young woman.
Ziel dieser Arbeit ist es, einen prägnanten Überblick über die Auslegungsgeschichte des Psalms 82 seit Beginn der historisch-kritischen Exegese Anfang des 19. Jahrhunderts zu geben. das Hauptaugenmerk liegt hierbei auf der Frage nach der Entstehungszeit des Psalms und dem zeitgeschichtlichen Kontext. Darüber hinaus sind die vorgenommene Deutung der im Text genannten "Götter" sowie die literarkritische Position der jeweiligen Ausleger im Blickfeld der Untersuchung.
Lung cancer is currently the leading cause of cancer related mortality due to late diagnosis and limited treatment intervention. Non-coding RNAs are not translated into proteins and have emerged as fundamental regulators of gene expression. Recent studies reported that microRNAs and long non-coding RNAs are involved in lung cancer development and progression. Moreover, they appear as new promising non-invasive biomarkers for early lung cancer diagnosis. Here, we highlight their potential as biomarker in lung cancer and present how bioinformatics can contribute to the development of non-invasive diagnostic tools. For this, we discuss several bioinformatics algorithms and software tools for a comprehensive understanding and functional characterization of microRNAs and long non-coding RNAs.