216 research outputs found
En komparativ analyse av historiske og liturgiske fremstillinger av Thomas Becket fra middelalderen
No full textDenne oppgaven er en komparativ analyse av fremstillinger av Thomas Becket fra historiske og liturgiske kilder fra 1100-tallet. Det benyttes hermeneutisk tekstanalyse for å undersøke et utvalg historiske og liturgiske kilder som omhandler Thomas Becket. Først analyseres henholdsvis de historiske og liturgiske kildene hver for seg, før en sammenligning og diskusjon av fremstillingsmåtene blir gjort. I denne komparative analysen kommer det frem at de historiske og liturgiske kildene fremstiller Thomas Becket på ulike måter. Der de liturgiske kildene bygger opp rundt et kristent ideal, er de historiske kildene mer nyanserte og preges av forfatternes egne biaser.This thesis is a comparative analysis of representations of Thomas Becket from historical and liturgical sources from the 12th century. Hermeneutic text analysis is used to examine a selection of historical and liturgical sources that deal with Thomas Becket. First, the historical and liturgical sources are analyzed separately, before a comparison and discussion of the methods of representation is made. In this comparative analysis, it emerges that the historical and liturgical sources portray Thomas Becket in different ways. Where the liturgical sources are built around a Christian ideal, the historical sources are more nuanced and characterized by the authors' own biases
EST based phylogenomics of Syndermata questions monophyly of Eurotatoria
No full textBackground: The metazoan taxon Syndermata comprising Rotifera (in the classical sense of Monogononta+Bdelloidea+Seisonidea) and Acanthocephala has raised several hypotheses connected to the phylogeny of these animal groups and the included subtaxa. While the monophyletic origin of Syndermata and Acanthocephala is well established based on morphological and molecular data, the phylogenetic position of Syndermata within Spiralia, the monophyletic origin of Monogononta, Bdelloidea, and Seisonidea and the acanthocephalan sister group are still a matter of debate. The comparison of the alternative hypotheses suggests that testing the phylogenetic validity of Eurotatoria (Monogononta+Bdelloidea) is the key to unravel the phylogenetic relations within Syndermata. The syndermatan phylogeny in turn is a prerequisite for reconstructing the evolution of the acanthocephalan endoparasitism. Results: Here we present our results from a phylogenomic approach studying i) the phylogenetic position of Syndermata within Spiralia, ii) the monophyletic origin of monogononts and bdelloids and iii) the phylogenetic relations of the latter two taxa to acanthocephalans. For this analysis we have generated EST libraries of Pomphorhynchus laevis, Echinorhynchus truttae (Acanthocephala) and Brachionus plicatilis (Monogononta). By extending these data with database entries of B. plicatilis, Philodina roseola (Bdelloidea) and 25 additional metazoan species, we conducted phylogenetic reconstructions based on 79 ribosomal proteins using maximum likelihood and bayesian approaches. Our findings suggest that the phylogenetic position of Syndermata within Spiralia is close to Platyhelminthes, that Eurotatoria are not monophyletic and that bdelloids are more closely related to acanthocephalans than monogononts. Conclusion: Mapping morphological character evolution onto molecular phylogeny suggests the (partial or complete) reduction of the corona and the emergence of a retractable anterior end (rostrum, proboscis) before the separation of Acanthocephala. In particular, the evolution of a rostrum might have been a key event leading to the later evolution of the acanthocephalan endoparasitism, given the enormous relevance of the proboscis for anchoring of the adults to the definitive hosts' intestinal wall.Deutsche Forschungsgemeinschaft DFG [Ha 2103/4-1, SPP1174
All-Food-Sequencing: Identification and quantification of food ingredients by whole-genome metagenomics
No full textAll-food sequencing (AFS) is a non-targeted, whole-genome DNA-based screening method for simultaneous qualitative and quantitative species diagnosis in complex foods. No a priori knowledge or primers are required, and a single analysis can potentially detect animal and plant components as well as fungi, bacteria, and other accompanying microbiota.
Quantitative performance of AFS was evaluated using controlled calibration samples, including defined meat and fish mixtures. In direct comparison with established assays, AFS delivered quantification that outperformed conventional qPCR and matched ddPCR, while retaining a key practical advantage: broad, primer-independent screening and quantification of multiple ingredients within a single workflow, rather than many separate target specific assays. The calibration series also identified two systematic factors that influence quantitative accuracy. First, differences in genome size can shift read proportions, but this bias was shown to be correctable by genome size normalization. Second, matrix effects of the food composition can alter DNA extraction yield between ingredients, so the highest quantitative agreement is achieved with matrix-specific calibration - a constraint shared by all DNA-based methods.
Application for real food products showed how AFS behaves under practical conditions with regard to heterogeneity and incomplete or inaccurate labelling of species components. Doner kebab samples showed significant deviations and several cases in which the predominant meat type did not correspond to the advertised expectation. In addition, other ingredients were detected that suggest unintentional admixture or deliberate substitution. In the case of seafood and surimi products, the declared main ingredients were generally confirmed. In addition, the analysis revealed undeclared taxa, including additional seafood and plant components in mixed dishes, some with potential allergen relevance. Beyond the main ingredient composition, AFS provided early warning signals, including allergen-relevant plant admixtures and microbial patterns that indicate incipient spoilage.
The analysed samples also revealed practical limitations of AFS that are crucial for regulatory surveillance: ambiguous classification within closely related species, dependence on reference genomes, and the need to interpret low-level findings conservatively and verify them with targeted follow-up measures. Specificity of read classification was improved by both algorithm choice and sequencing technology. K-mer-based classification and database partitioning enabled screening against significantly larger genome reference collections. In a comparison between Illumina short reads and Oxford Nanopore long reads on calibration sausages, long-read sequencing improved quantification accuracy and reduced the number of false-positives despite higher error rates in long read, as longer reads provide more discriminative information for resolving conserved regions that otherwise drive ambiguous classification.
AFS shows the potential to provide reliable formulation information and cross-domain early warning signals as a universal, primer-free WGS screening method, provided that reference dependency and taxonomic ambiguity are recognized as current limitations and integrated into the decision on verification or follow-up measures. Therefore, it is promising for routine screening in official food monitoring in the future.xii, 193 Seiten ; Illustrationen, Diagramm
Identification of structural variations from whole genome sequencing of cancer patients
No full textCancer is largely driven by accumulation of somatic mutations that can be subdivided into small mutations (single nucleotide variations (SNVs), small insertions and deletions) and large structural variations (SVs). While SNVs affect single nucleotide, SVs can affect large stretches of DNA. Reliable identification of all mutations is key to understanding genetic diseases like cancer.
SVs can be identified by whole genome sequencing with conventional Illumina short-read sequencing (cWGS) being the most widely used approach. However, reliable prediction of SVs with short-reads (50-150bp) from fragmented DNA (~0.5kb) is challenging due to ambiguous mapping reads at repetitive regions and typically only few short reads span rearranged SV breakpoints with limited sequence overlap (due to read length). The 10X Genomics linked- reads sequencing (10XWGS) technology aims to mitigate limitations by linking short-reads to the original larger fragment of DNA (~10kb). In this study, we performed an unbiased evaluation of these two technologies with different types and sizes of SVs and compared their performance. The SVs commonly identified by both the technologies were highly specific, while the validation rate dropped for uncommon SVs. Despite the technological advantage, a particularly high false discovery rate (FDR) was observed for SVs found only by 10XWGS without any significant improvement in sensitivity. We proposed a sensitive and specific statistical approach to improve SV predictions from both technologies and characterized SVs from MCF7 breast cancer cell line and a primary breast tumor with high precision.
Due to the limited benefit of 10XWGS for sensitivity, we trained a random forest classifier in FuseSV for accurate predictions only from cWGS sequencing data. FuseSV integrates SV predictions from multiple bioinformatics tools and mitigates high FDR of cWGS with a novel set of features derived from alignment of reads to the reference genome, biological mechanisms of SVs and breakpoints of SVs clustered together to consider complex genomic rearrangements (CGRs). The performance of FuseSV classifiers was superior to all individual bioinformatics tools as well as combined use with 10XWGS.
SVs whether simple or complex can form chimeric fusion transcripts (CMTs). CMTs can be predicted from RNA-sequencing (RNA-seq) data but include also transcripts that occur without underlying mutation and are also present in healthy tissues. Here we propose a novel pipeline, FUdGE, that predict three types of CMT directly from somatic SVs: These include direct fusion transcripts or classical fusion genes, transcripts with intron (IR) and intergenic region retained (INR). FUdGE allows independent confirmation of expressed CMTs from matched RNA-seq data. We validated the approach in the same MCF7 cell line and a primary breast tumor sample and investigate CMTs in a cohort of liposarcoma samples. Here we observed that the majority of confirmed SV driven CMTs were classical fusion genes with a much smaller number of IR and INR events.
Conclusively, FuseSV enables accurate prediction of somatic SVs in cancer using only cWGS. While FUdGE provides an RNA-seq independent strategy for direct prediction of CMTs formed due to somatic SV event. The respective expressed CMT candidates can be confirmed independently with RNA-seq data. This alternative approach only predicts tumor-specific somatic SV driven CMTs, which is advantageous for personalized immunotherapy interventions considering CMTs as neo-antigen candidates.XII, 91 Seiten ; Illustrationen, Diagramm
Human models for White Sutton syndrome: POGZ mutations change the transcriptome and induce defects in neural progenitor cell biology
No full textIntellectual disability (ID) and autism spectrum disorders (ASD) are complex neurodevelopmental conditions with high genetic heterogeneity. Studies indicate that 10%-40% of individuals with ID also have ASD, suggesting shared molecular mechanisms between these disorders. Recent next-generation sequencing studies have highlighted a significant role of de novo mutations in ASD, particularly those with large effects. Among these, POGZ (Pogo Transposable Element with zinc finger “ZNF” domain) has emerged as a frequently mutated gene with potential loss-of-function effects in ASD patients. However, the underlying molecular mechanisms and the pathogenic impact of POGZ mutations are not fully understood.
POGZ encodes a protein that is mainly binds to heterochromatin protein 1α and contributes to gene regulatory functions. Functionally, POGZ is critical for kinetochore assembly, sister chromatid cohesion, and mitotic chromosome segregation. POGZ deficiency can lead to premature mitotic exit, polyploidy, and potential cell death or genomic instability, which may disrupt neural development and brain function. POGZ thought to act as a transcriptional regulator, potentially influencing molecular networks that are critical for neuronal function.
This PhD study investigated the cellular and molecular mechanisms by which POGZ mutations contribute to neurodevelopmental disorders (NDDs) using human induced pluripotent stem cells (iPSCs) derived from patient and CRISPR/Cas9-mediated gene editing to introduce heterozygous POGZ mutations. These mutant iPSCs were differentiated into neural progenitor cells (NPCs) and neurons under both two-dimensional (2D) and three-dimensional (3D) culture conditions to analyze the effects of POGZ mutations on neural development.
Key findings of the study indicated that frameshift mutations in the N-terminus or the HP1-binding zinc finger-like (HPZ) domain of POGZ led to decreased POGZ protein expression without disrupting its nuclear localization. Using 3D neurospheres and brain organoids, it was found that POGZ-deficient cells exhibited impaired self-renewal of NPCs, alongside enhanced differentiation and increased neuronal migration. Additionally, analysis of the transcriptome via RNA sequencing revealed widespread changes in gene expression in NPCs carrying POGZ mutations. These alterations were significantly enriched for genes involved in mitotic chromatid segregation, DNA repair, nonsense-mediated decay, and alternative splicing. Notably, the data revealed a transcriptomic signature characterized by the elevated expression of neuron-specific genes, suggesting an "accelerated differentiation" phenotype in mutant NPCs, mirroring the behavior observed in the 3D neurosphere models.
Furthermore, CUT&Tag sequencing was employed to identify direct targets of POGZ, providing evidence that POGZ directly regulated genes linked to synaptic function, chromosome segregation, and Wnt signaling. The overrepresentation of autism-associated risk genes among POGZ-regulated targets further suggested a potential link between POGZ dysfunction and the etiology of NDDs, including ASD.
This analysis emphasized the critical role of POGZ in regulating neural development at both the cellular and molecular levels. Understanding how POGZ mutations drive alterations in NPC behavior and gene regulation, is crucial for developing targeted therapeutic strategies for conditions associated with POGZ dysfunction. Ultimately, this study aimed to bridge the gap between genetic findings and pathophysiological mechanisms in NDDs, providing deeper insights into the developmental disruptions caused by POGZ mutations.197 Seiten ; Illustrationen, Diagramm
Towards the role of the skin microbiome in the aetiopathogenesis of cutaneous T-Cell Lymphoma
No full textMycosis fungoides (MF) is the most common form of cutaneous T-cell lymphoma (CTCL), a heterogeneous group of non-Hodgkin lymphomas with primary skin involvement. Its aetiopathogenesis remains incompletely understood, partly due to pronounced clinical and transcriptional heterogeneity. This cumulative dissertation presents a multi-omics investigation into the role of the skin microbiome in MF pathobiology, encompassing metagenomic, transcriptomic, virologic, and T-cell receptor (TCR) sequencing data from patient-matched lesional and nonlesional skin. In addition, functional assays were performed on patient-derived skin isolates.
Publication 1 reviews the interplay between transcriptional heterogeneity and the skin microbiota in CTCL, proposing a reciprocal relationship between neoplastic T-cell signalling and microbial colonisation.
Publication 2 provides the first conclusive evidence for taxonomic and functional microbiome shifts on MF skin. It identifies a distinct subgroup of patients (ΔSA-positive) with increased lesional abundance of Staphylococcus aureus, reduced microbial diversity, a restricted TCR repertoire, and inferior clinical outcome. Lesional isolates of ΔSA-positive S. aureus exhibited resistance to cutaneous antimicrobial peptides, which were ectopically expressed and may have contributed to commensal flora eradication. This strain also harboured mutant spa, a virulence factor known to activate NF-κB signalling, thereby supporting a functional role in disease progression.
Publication 3 shows that transcriptional heterogeneity may reflect differences in T-cell signalling activity. Multi-omic data integration revealed ΔSA-positive S. aureus strain-driven activation of non-canonical NF-κB and IL-1β signalling, both implicated in T-cell activation and MF progression. Importantly, denoising the skin transcriptome from microbial influence resolved the observed differential expression pattern. Additionally, antiviral signatures and Epstein–Barr virus reactivity in blood and skin suggest a two-hit model of MF aetiopathogenesis involving viral and bacterial triggers.
Together, this thesis positions the skin microbiome as a clinically relevant modulator of MF biology. The findings support S. aureus as a potential prognostic biomarker and therapeutic target and lay the groundwork for microbiome-informed precision medicine.XI, 206 Seiten : Illustrationen, Diagramm
Human neuroglobin: crystals and preliminary X-ray diffraction analysis.
No full textNeuroglobin, a recently discovered member of the haemoglobin superfamily, is primarily expressed in the brain of humans and other vertebrates, where it has been proposed to enhance O(2) supply in response to hypoxia or ischaemia, protecting the neuron from hypoxic injury. Neuroglobin is the first example of a vertebrate haemoglobin in which a hexacoordinate haem geometry has been detected. A triple mutant (replacing three Cys residues) of human neuroglobin (151 amino acids) has been expressed in Escherichia coli, purified and crystallized in two crystal forms, the best of which diffracts to 1.95 A resolution using synchrotron radiation. The crystals belong to space group P2(1), with unit-cell parameters a = 39.6, b = 94.9, c = 67.5 A, beta = 94.4 degrees, and contain 2-4 protein molecules per asymmetric unit
Reversible hexa- to penta-coordination of the heme Fe atom modulates ligand binding properties of neuroglobin and cytoglobin
No full textNeuroglobin (Ngb) and cytoglobin (Cygb) are two recently
discovered intracellular members of the vertebrate hemoglobin (Hb)
family. Ngb, predominantly expressed in nerve cells, is of ancient
evolutionary origin and is homologous to nerve-globins of
invertebrates. Cygb, present in many different tissues, shares
common ancestry with myoglobin (Mb) and can be traced to early
vertebrate evolution. Ngb is held to facilitate O2 diffusion to the
mitochondria and to protect neuronal cells from hypoxic-ischemic
insults, may be an oxidative stress-responsive sensor protein for
signal transduction, and may carry out enzymatic activities, such as
NO/O2 scavenging. Cygb is linked to collagen synthesis, may
provide O2 for enzymatic reactions, and may be involved in a ROS
(NO)-signaling pathway(s). Ngb and Cgb display the classical threeover-
three a-helical fold of Hb and Mb, and are endowed with a
hexa-coordinate heme-Fe atom, in their ferrous and ferric forms,
having the heme distal HisE7 residue as the endogenous ligand.
Reversible hexa- to penta-coordination of the heme Fe atom
modulates ligand binding properties of Ngb and Cygb. Moreover,
Ngb and Cygb display a tunnel/cavity system within the protein
matrix held to facilitate ligand channeling to/from the heme,
multiple ligand copies storage, multi-ligand reactions, and
conformational transitions supporting ligand binding
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