Refine
Year of publication
- 2019 (222) (remove)
Document Type
- Article (167)
- Doctoral Thesis (55)
Language
- English (222) (remove)
Has Fulltext
- yes (222)
Is part of the Bibliography
- no (222)
Keywords
- - (114)
- proteomics (7)
- metabolomics (4)
- periodontitis (4)
- <i>Staphylococcus aureus</i> (3)
- Caries epidemiology (3)
- Caries experience (3)
- Proteomics (3)
- Streptococcus pneumoniae (3)
- <i>Bacillus subtilis</i> (2)
Institute
- Abteilung für Mikrobiologie und Molekularbiologie (19)
- Institut für Biochemie (16)
- Institut für Geographie und Geologie (16)
- Institut für Physik (14)
- Institut für Pharmazie (13)
- Institut für Botanik und Landschaftsökologie & Botanischer Garten (10)
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung (MNF) (10)
- Kliniken und Polikliniken für Innere Medizin (10)
- Zoologisches Institut und Museum (10)
- Klinik und Poliklinik für Neurologie (8)
Publisher
- MDPI (53)
- Frontiers Media S.A. (29)
- S. Karger AG (20)
- Copernicus (12)
- SAGE Publications (11)
- Wiley (9)
- Public Library of Science (PLoS) (7)
- BioMed Central (BMC) (4)
- De Gruyter (4)
- Nature Publishing Group (4)
In phylogenetics, evolutionary relationships of different species are represented by phylogenetic trees.
In this thesis, we are mainly concerned with the reconstruction of ancestral sequences and the accuracy of this reconstruction given a rooted binary phylogenetic tree.
For example, we wish to estimate the DNA sequences of the ancestors given the observed DNA sequences of today living species.
In particular, we are interested in reconstructing the DNA sequence of the last common ancestor of all species under consideration. Note that this last common ancestor corresponds to the root of the tree.
There exist various methods for the reconstruction of ancestral sequences.
A widely used principle for ancestral sequence reconstruction is the principle of parsimony (Maximum Parsimony).
This principle means that the simplest explanation it the best.
Applied to the reconstruction of ancestral sequences this means that a sequence which requires the fewest evolutionary changes along the tree is reconstructed.
Thus, the number of changes is minimized, which explains the name of Maximum Parsimony.
Instead of estimating a whole DNA sequence, Maximum Parsimony considers each position in the sequence separately. Thus in the following, each sequence position is regarded separately, and we call a single position in a sequence state.
It can happen that the state of the last common ancestor is reconstructed unambiguously, for example as A. On the other hand, Maximum Parsimony might be indecisive between two DNA nucleotides, say for example A and C.
In this case, the last common ancestor will be reconstructed as {A,C}.
Therefore we consider, after an introduction and some preliminary definitions, the following question in Section 3: how many present-day species need to be in a certain state, for example A, such that the Maximum Parsimony estimate of the last common ancestor is also {A}?
The answer of this question depends on the tree topology as well as on the number of different states.
In Section 4, we provide a sufficient condition for Maximum Parsimony to recover the ancestral state at the root correctly from the observed states at the leaves.
The so-called reconstruction accuracy for the reconstruction of ancestral states is introduced in Section 5. The reconstruction accuracy is the probability that the true root state is indeed reconstructed and always takes two processes into account: on the one hand the approach to reconstruct ancestral states, and on the other hand the way how the states evolve along the edges of the tree. The latter is given by an evolutionary model.
In the present thesis, we focus on a simple symmetric model, the Neyman model.
The symmetry of the model means for example that a change from A to C is equally likely than a change from C to A.
Intuitively, one could expect that the reconstruction accuracy it the highest when all present-day species are taken into account. However, it has long been known that the reconstruction accuracy improves when some taxa are disregarded for the estimation.
Therefore, the question if there exits at least a lower bound for the reconstruction accuracy arises, i.e. if it is best to consider all today living species instead of just one for the reconstruction.
This is bad news for Maximum Parsimony as a criterion for ancestral state reconstruction, and therefore the question if there exists at least a lower bound for the reconstruction accuracy arises.
In Section 5, we start with considering ultrametric trees, which are trees where the expected number of substitutions from the root to each leaf is the same.
For such trees, we investigate a lower bound for the reconstruction accuracy, when the number of different states at the leaves of the tree is 3 or 4.
Subsequently in Section 6, in order to generalize this result, we introduce a new method for ancestral state reconstruction: the coin-toss method.
We obtain new results for the reconstruction accuracy of Maximum Parsimony by relating Maximum Parsimony to the coin-toss method.
Some of these results do not require the underlying tree to be ultrametric.
Then, in Section 7 we investigate the influence of specific tree topologies on the reconstruction accuracy of Maximum Parsimony. In particular, we consider balanced and imbalanced trees as the balance of a tree may have an influence on the reconstruction accuracy.
We end by introducing the Colless index in Section 8, an index which measures the degree of balance a rooted binary tree can have, and analyze its extremal properties.
Spinal cord injury (SCI) above mid-thoracic levels leads to autonomic dysfunction affecting both the cardiovascular system and thermoregulation. The renin-angiotensin system (RAS) which is a potent regulator of blood pressure, including its novel beneficial arm with the receptor Mas could be an interesting target in post-SCI hemodynamics. To test the hypothesis that hemodynamics, activity and diurnal patterns of those are more affected in the Mas deficient mice post-SCI we used a mouse model of SCI with complete transection of spinal cord at thoracic level 4 (T4-Tx) and performed telemetric monitoring of blood pressure (BP) and heart rate (HR). Our data revealed that hypothermia deteriorated physiological BP and HR control. Preserving normothermia by keeping mice at 30°C prevented severe hypotension and bradycardia post-SCI. Moreover, it facilitated rapid return of diurnal regulation of BP, HR and activity in wild type (WT) mice. In contrast, although Mas deficient mice had comparable reacquisition of diurnal HR rhythm, they showed delayed recovery of diurnal rhythmicity in BP and significantly lower nocturnal activity. Exposing mice with T4-Tx (kept in temperature-controlled cages) to 23°C room temperature for one hour at different time-points post-SCI, demonstrated their inability to maintain core body temperature, Mas deficient mice being significantly more impaired than WT littermates. We conclude that Mas deficient mice were more resistant to acute hypotension, delayed nocturnal recovery, lower activity and more severely impaired thermoregulation. The ambient temperature had significant effect on hemodynamics and, thus it should be taken into account when assessing cardiovascular parameters post-SCI in mice.
Summary
The susceptibility of Candida albicans biofilms to a non‐thermal plasma treatment has been investigated in terms of growth, survival and cell viability by a series of in vitro experiments. For different time periods, the C. albicans strain SC5314 was treated with a microwave‐induced plasma torch (MiniMIP). The MiniMIP treatment had a strong effect (reduction factor (RF) = 2.97 after 50 s treatment) at a distance of 3 cm between the nozzle and the superior regions of the biofilms. In addition, a viability reduction of 77% after a 20 s plasma treatment and a metabolism reduction of 90% after a 40 s plasma treatment time were observed for C. albicans. After such a treatment, the biofilms revealed an altered morphology of their cells by atomic force microscopy (AFM). Additionally, fluorescence microscopy and confocal laser scanning microscopy (CLSM) analyses of plasma‐treated biofilms showed that an inactivation of cells mainly appeared on the bottom side of the biofilms. Thus, the plasma inactivation of the overgrown surface reveals a new possibility to combat biofilms.
Introduction: Hearing and vision loss are highly prevalent in elderly adults, and thus frequently occur in conjunction with cognitive impairments. Studies have shown that hearing impairment is associated with a higher risk of dementia. However, evidence concerning the association between vision loss and dementia, as well as the co-occurrence of vision and hearing loss and dementia, has been inconclusive.
Objectives: To assess the association between: (i) either hearing or vision loss and the risk of dementia, as well as between; and (ii) the combination of both sensory impairments and the risk of dementia.
Methods: This case-control study was based on a 5-year data set that included patients aged 65 years and older who had initially been diagnosed with dementia diseases by one of 1,203 general practitioners in Germany between January 2013 and December 2017. In total, 61,354 identified dementia cases were matched to non-dementia controls, resulting in a sample size of 122,708 individuals. Hearing loss and vision loss were identified using the ICD-10 diagnoses documented in the general practitioners’ files prior to the initial dementia diagnosis. Multivariate logistic regression models were fitted to evaluate the associations between visual and/or hearing impairment and the risk of dementia and controlled for sociodemographic and clinical variables.
Results: Hearing impairment was documented in 11.2% of patients with a dementia diagnosis and 9.5% of patients without such a diagnosis. Some form of vision impairment was documented in 28.4% of patients diagnosed with dementia and 28.8% of controls. Visual impairment was not significantly associated with dementia (OR = 0.97, CI = 95% 0.97–1.02, p = 0.219). However, patients with hearing impairment were at a significantly higher risk of developing dementia (OR = 1.26, CI = 95% 1.15–1.38, p < 0.001), a finding that very likely led to the observed significant association of the combination of both visual and hearing impairments and the risk of dementia (OR = 1.14, CI = 95% 1.04–1.24, p = 0.005).
Discussion: This analysis adds important evidence that contributes to the limited body of knowledge about the association between hearing and/or vision loss and dementia. It further demonstrates that, of the two, only hearing impairment affects patients’ cognition and thus contributes to dementia risk.
Brain aging even in healthy older adults is characterized by a decline in cognitive functions including memory, learning and attention. Among others, memory is one of the major cognitive functions affected by aging. Understanding the mechanisms underlying age-related memory decline may help pave the road for novel treatment strategies. Here, we tried to elucidate the neural correlates associated with memory decline using structural and functional neuroimaging and neuromodulation with transcranial direct current stimulation (tDCS).
Over the course of three studies, we investigated 1) the influence of white matter integrity and grey matter volume on memory performance in healthy older adults, 2) the role of functional coupling within the memory network in predicting memory performance and the impact of tDCS in modulating retrieval performance in healthy older adults, 3) the effect of tDCS over the sensorimotor cortex on cognitive performance in young adults.
MRI was used to study associations of cognitive performance with white matter integrity and grey matter volume, and examine their causal relationship in the course of aging. White matter integrity was assessed by acquiring diffusion tensor imaging (DTI) and performing deterministic tractography based on constrained spherical deconvolution. Grey matter volume was estimated using fully automated segmentation. Both white matter integrity and grey matter volume were correlated with behavioral data of a verbal episodic memory task. Percentage of correct answers at retrieval was used to measure memory performance (Manuscript 1). In addition, anodal tDCS (atDCS) (1 mA, 20 min) was applied over CP5 (left temporoparietal cortex) to modulate memory formation in healthy older adults. Participants underwent resting-state fMRI before the stimulation. Functional connectivity analysis was performed to determine whether functional coupling within the memory network predicted initial memory performance, and to examine its association to tDCS-induced enhancement effect (Manuscript 2). Finally, atDCS (1 mA, 20 min) was applied over C3 (left sensorimotor cortex) to explore the effect of tDCS over the sensorimotor cortex on cognitive performance in young adults. During the stimulation, participants performed three tasks; gestural task, attentional load task and simple reaction time task (Manuscript 3).
Results showed that volumes of the left dentate gyrus (DG) and tractography-based fractional anisotropy (FA) of individual fornix pathways were positively related to memory retrieval in older adults. Brain-behavior associations were observed for correct rejections rather than hits of memory performance, indicating specificity of memory network functioning for detecting false associations. Thus, the data suggested a particular role of neural integrity that promotes successful memory retrieval in older adults. Subsequent mediation analysis showed that left DG volume mediated the effect of fornix FA on memory performance (48%), corrected for age, revealing a crucial role of hippocampal pathway microstructure in modulating memory performance in older adults (Manuscript 1). tDCS results showed that atDCS led to better retrieval performance and increasing learning curves, indicating that brain stimulation can induce plasticity of episodic memory processes in older adults. Combining tDCS and fMRI, hippocampo-temporoparietal functional connectivity was positively associated with initial memory performance in healthy older adults and was positively correlated with the magnitude of individual tDCS-induced enhancement, suggesting that individual tDCS responsiveness may be determined by intrinsic network coupling (Manuscript 2). Finally, our findings suggested that atDCS over left sensorimotor cortex reduced reaction times in the gestural-verbal integration task, specifically for incongruent pairs of gestures and verbal expressions, indicating the role of sensorimotor cortex in gestural-verbal integration in young adults (Manuscript 3).
The results of all three studies may help to elucidate age-related structural deterioration and functional coupling network underlying cognitive processes in healthy adults. Furthermore, these studies emphasized the importance of interventions like tDCS in modulating cognitive performance, specifically episodic verbal memory and gestural-verbal integration. By unveiling the specific role of brain structures and functional network coupling as well as the role of tDCS in modulating cognitive performance, our results contribute to a better understanding of brain-behavior associations, and may help to develop clinical interventional approaches, tailored for specific cognitive functions in aging.
In this thesis, we elaborate upon Bayesian changepoint analysis, whereby our focus is on three big topics: approximate sampling via MCMC, exact inference and uncertainty quantification. Besides, modeling matters are discussed in an ongoing fashion. Our findings are underpinned through several changepoint examples with a focus on a well-log drilling data.