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Detection and functional annotation of unique genomic regions
Get PDFEvery organism has a genome. In some organisms, like mammals, genomes are highly repetitive. Repetitive genomic regions are associated with multiple biological functions as they can influence genome organization and gene regulation. Therefore, considerable importance is placed on identifying, localizing and categorizing them. Perhaps less studied but also important is the identification and categorization of unique genomic regions. Although unique regions have been associated with housekeeping and developmental genes and are thus crucial for survival, there is a distinct lack of bioinformatic tools for specifically finding unique regions in genomic sequences. This thesis explores existing tools for finding unique genomic regions, expands their application domains, and establishes workflows for applying them in comparative genomics. This thesis also contributes to the toolkit of comparative genomics by improving existing tools and integrating them into scaleable workflows for the detection of unique regions. Once detected, the unique regions are investigated for their functional content in mammals (Chapters 2 and 4), and for their suitability as diagnostic markers in bacteria (Chapter 3)
Molekularbiologische und immunhistochemische Untersuchung der Schadenskaskade in neuroepithelialem Gewebe in einem Rattenmyelomeningozelenmodell zu verschiedenen Zeitpunkten im embryonalen Verlauf
Get PDFIn der Entwicklung innovativer Therapiekonzepte zur Versorgung von MMC-Patienten ist das Verständnis der zellulären und molekularen Vorgänge in der Plakode essenziell. Neben dem strukturellen Defekt der fehlerhaften Neurulation sind durch sekundäre Traumata angestoßene Läsionskaskaden im Sinne der Second-/Third-Hit-Hypothese zu bedenken. Die bisherige Datenlage bezüglich der zugrundeliegenden, zellulären Schädigungsmechanismen ist sehr dünn. Insbesondere der Zeitpunkt der Induktion dieser Mechanismen sowie deren potentiell pränataler Verlauf sind wenig verstanden. Die vorliegende Arbeit hatte zum Ziel, erstmals einen Einblick zu gewinnen in die pränatale Dynamik der Schädigungskaskade. Dies erfolgte im Rahmen eines Rattenmyelomeningozelenmodells durch molekularbiologische, histologische und immunhistochemische Analyse des Plakodengewebes zu verschiedenen Zeitpunkten im späten, fetalen Verlauf. Zum perinatalen Zeitpunkt E22 zeigten sich erhöhte mRNA-Expressionslevel von IL-1β und TNF-α sowie derer Rezeptoren. Auch in den immunhistochemischen Färbungen zeigte sich zum Zeitpunkt E22 eine erhöhte Immunoreaktivität für die Zytokine und ihre Rezeptoren. In den Doppelimmunfluoreszenzfärbungen offenbarten sich sowohl Neurone, radiäre Glia/Astrozyten und Mikroglia als Träger der Schädigungsmechanismen, wobei letztere die deutlichste Immunoreaktivität zeigten. Somit bestätigte sich, dass die zellulären und molekularen Veränderungen, welche im Rahmen traumatischer Rückenmarksschädigung von entscheidender Bedeutung sind, auch im neuroepithelialen Gewebe eine wichtige Rolle spielen. Diese Mediatoren könnten folglich für den bei MMC-Patienten beobachteten Verlust neurologischer Funktion sowie für histopathologische Veränderungen in der späten Gestationsphase verantwortlich sein
First record of the foraminiferal species Ammonia confertitesta in southeastern Baltic sea
Get PDFEarly identification of non-indigenous species is important, as they have the potential to disrupt biogeochemical cycles, ecosystem stability, and trophic energy transfer in fragile ecosystems. Non-indigenous species may impact the functioning of the Baltic Sea ecosystem, the largest brackish water body in the world. This study presents the first record of the non-indigenous Asian foraminiferal species Ammonia confertitesta in the southeastern Baltic Sea. The species was recorded at 6 out of 14 sampling stations in the Gulf of Gdańsk, Poland, with one station sampled several times throughout the year, where A. confertitesta was consistently present. The species was also found in Puck Bay, a shallow western branch of the Gulf of Gdańsk. Our finding marks the first modern record of the genus Ammonia in the southeastern Baltic Sea. It provides new evidence for the rapid spread of A. confertitesta in European waters, highlighting its ability to thrive in environments where other calcareous foraminiferal species face difficulties. Morphometric comparisons with a population of the same species found in the western Baltic Sea shows that the Gulf of Gdańsk specimens are smaller. This may indicate that the species has reached its limits of environmental tolerance. However, given the increasing abundance of A. confertitesta in the Gulf of Gdańsk, it is important to monitor its further progression and investigate its long-term ecological impact on native species and the Baltic Sea ecosystem
Sediment resuspension in muddy sediments enhances pyrite oxidation and carbon dioxide emissions in Kiel Bight
Get PDFSediment resuspension of blue carbon ecosystems (e.g., seagrass beds) and muddy sediments exposes buried particulate organic carbon to oxygenated waters and remineralization, potentially enhancing carbon dioxide fluxes. However, the kinetics of carbon degradation under oxic and anoxic conditions are poorly constrained. We report the results of incubation experiments with sediments from Kiel Bight to simulate sediment resuspension events induced by natural and anthropogenic resuspension in this area. A numerical model determined that oxic carbon remineralization rates were up to two-fold higher than those under anoxic conditions. A coupled sediment-water column model demonstrated that pyrite oxidation, rather than carbon oxidation, has the potential to induce large carbon dioxide emissions to the atmosphere following anthropogenic sediment disturbance by trawling. Upscaling to muddy areas of Kiel Bight suggests an annual emission of up to ~14 k tonnes of carbon dioxide per year. Pyrite oxidation may contribute to a weakening of the carbon shelf pump and a reduction of anthropogenic carbon dioxide uptake
Local Adaptation and Osmoregulatory Mechanisms of the Copepod Acartia tonsa Under Low Salinity Stress
Get PDFSalinity—an essential factor shaping marine species distributions—is rapidly shifting due to global change, yet the mechanisms of salinity tolerance and adaptation remain poorly understood. We investigated local adaptation in the calanoid copepod Acartia tonsa, a broadly distributed marine species that thrives in the brackish Baltic Sea. Using a common-garden design, we compared physiological and transcriptomic responses to low salinity between populations from the North Sea (> 25 PSU) and the Baltic Sea (< 15 PSU). Baltic copepods exhibited significantly higher survival under low salinity, indicating local adaptation. While both populations shared a core osmoregulatory strategy involving active ion transport and regulation of amino acids, transcriptomic profiles revealed population-specific differences. Baltic individuals showed a reduced overall gene expression response, yet maintained higher relative expression of osmoregulatory genes—suggesting a more efficient and primed transcriptomic response. In contrast, North Sea copepods exhibited broader transcriptional shifts, including downregulation of metabolic and developmental pathways after prolonged stress exposure, possibly reflecting energy conservation mechanisms. These findings reveal that A. tonsa possesses both a plastic osmoregulatory strategy and population-level adaptation that enable survival in extreme salinity conditions. While both populations tolerate short-term exposure to low salinity, local adaptation has enhanced the Baltic population's resilience. This suggests that A. tonsa is broadly tolerant of moderate climate-driven salinity declines across most of its distribution. However, our data also indicate potential range contractions in the lowest salinity zones of the Baltic Sea, underscoring the importance of identifying physiological and genetic thresholds in climate resilience studies
Evaluating the Validity of the Student Perspectives of Teaching Survey: A Network Psychometrics Approach
Get PDFHigher education institutions commonly employ student evaluation of teaching (SET) instruments (e.g., course evaluation surveys) to enhance course quality and inform instructional strategies. However, conceptualizing and measuring SET as a unidimensional construct may compromise validity, particularly when represented by a single aggregated score. This study uses a network psychometrics approach to explore the validity of a new instrument that acknowledges the multidimensional nature of SET as an educational construct. The central research question is, “How is the robustness of a multidimensional students’ evaluation of the teaching survey?”. The study sample consists of 649 undergraduate students from a western Canadian university who completed a multidimensional SET instrument. The instrument consists of six subscales corresponding to six aspects of SET (i.e., design, utility of course resources, graded work, course delivery, instructional approach, and class climate). The findings revealed a robust line of evidence that supports the validity of the instrument’s interpretation and usage. This was demonstrated through a high coefficient alpha, good network model fit, and stable survey structure. The study provides evidence supporting the use of a multidimensional SET instrument and offers novel validity support via the structural evidence provided by network analysis
Design, Synthese und Charakterisierung von Triphenylen- und Imid-Diazocinen mit verbesserten Eigenschaften zur Anwendung in intelligenten Materialien
No full textThis dissertation is dedicated to the development, investigation, and application of novel photoswitchable systems based on diazocines. The focus is on the synthesis and characterization of two structural classes of derivatives, previously unreported in the literature, namely tetrasubstituted triphenylene diazocines and disubstituted cyclic-imide diazocines. Introduction of functional groups is facile by late-stage derivatization of the diazocine. Both classes of compounds undergo a photoinduced, wing-flapping-like, and reversible Z ⇆ E isomerization associated with a large switching amplitude, which makes these systems particularly attractive for use as actuators in photo- and mechanoresponsive materials. Preliminary results from the incorporation of an unsaturated derivative into a liquid-crystalline elastomer film demonstrate photothermally driven macroscopic motion of the material. The triphenylene diazocines feature large annulated aromatic ring systems with a characteristic tub-shaped arrangement in the Z configuration. The possibility to incorporate four long-chain aliphatic substituents renders them promising candidates for application in photosensitive columnar liquid crystals, which is supported by X-ray crystal structures. The imide diazocines exhibit a novel substitution pattern that aligns almost exactly with the molecular stretching and bending vectors during photoisomerization, which is supported by theoretical modeling and X-ray crystal structures. This geometry is particularly well-suited for photoactuators and molecular tweezers in supramolecular host-guest systems. In total, four scientific articles were published, describing novel diazocines and precursors. Another scientific publication explores a silylation strategy for the fabrication of polymeric thin films using initiated chemical vapor deposition, which can be applied for the preparation of photoswitchable materials with hydrophilic diazocines
Lebenslinien zwischen Ideologie und Emanzipation: Selbstzeugnisse der Kolonialsiedlerin Ada Cramer (1874-1962) und der Heimatforscherin Helene Höhnk (1859-1944)
Get PDFDer Doppelband Lebenslinien zwischen Ideologie und Emanzipation entstand aus den Masterarbeiten von Felicia Engelhard und Anne Krohn, die sich mit den autobiographischen Selbstzeugnissen der Kolonialsiedlerin Ada Cramer in Deutsch-Südwestafrika und der Dithmarscher Heimatforscherin Helene Höhnk beschäftigten. Die hier gemeinsam vorgelegten Untersuchungen richten ihr Erkenntnisinteresse auf die Frage, wie die Autorinnen in den ideologisch geprägten Kontexten der ersten Hälfte des 20. Jahrhunderts ihre Erfahrungen, Überzeugungen und Handlungsspielräume autobiographisch deuteten und legitimierten. Während Felicia Engelhard am Beispiel Ada Cramers kolonialem Erlebnisbericht Weiß oder Schwarz (1913) die Verflechtung von Rassedenken, kolonialer Realität und Selbstrechtfertigung analysiert, zeigt Anne Krohn anhand von Helene Höhnks Lebenserinnerungen (1939), wie sich weibliche Selbstbehauptung im Spannungsfeld zwischen emanzipatorischem Anspruch und völkisch-nationaler Weltanschauung formiert. Der Band demonstriert, dass Emanzipation und Ideologie keine Gegensätze, sondern verflochtene Kräfte weiblicher Lebensgestaltung darstellen konnten.The two-volume edition Lebenslinien zwischen Ideologie und Emanzipation (Lifelines between Ideology and Emancipation) is based on the master's theses of Felicia Engelhard and Anne Krohn, which deal with the autobiographical accounts of colonial settler Ada Cramer in German South West Africa and local historian Helene Höhnk from Dithmarschen. The studies presented here focus on the question of how the authors interpreted and legitimized their experiences, beliefs, and agency autobiographically in the ideologically charged contexts of the first half of the 20th century. While Felicia Engelhard analyzes the interconnectedness of racial thinking, colonial reality, and self-justification using the example of Ada Cramer's colonial experience report Weiß oder Schwarz (1913), Anne Krohn uses Helene Höhnk's Lebenserinnerungen (1939) to show how female self-assertion took shape between emancipatory aspirations and a nationalist worldview. The volume shows that emancipation and ideology were not opposites, but rather intertwined forces in shaping women's lives
Association of real life postural transitions kinematics with fatigue in neurodegenerative and immune diseases
Get PDFFatigue is prevalent in immune-mediated inflammatory and neurodegenerative diseases, yet its assessment relies largely on patient-reported outcomes, which capture perception but not fluctuations over time. Wearable sensors, like inertial measurement units (IMUs), offer a way to monitor daily activities and evaluate functional capacity. This study investigates the relationship between sit-to-stand and stand-to-sit transitions and self-reported physical and mental fatigue in participants with Parkinson's, Huntington's, rheumatoid arthritis, systemic lupus erythematosus, primary Sjögren's syndrome and inflammatory bowel disease. Over 4 weeks, participants wore an IMU and reported fatigue levels four times daily. Using mixed-effects models, associations were identified between fatigue and specific kinematic features, such as 5th and 95th percentiles of sit-to-stand performance, suggesting that fatigue alters the control and effort of movement. These kinematic features show promise as indicators for fatigue in these patient populations
Identification of Quantitative Trait Loci (QTLs) and candidate genes for trichome development in Brassica villosa using genetic, genomic, and transcriptomic approaches
Get PDFBrassica villosa is characterized by its dense hairiness and high resistance against the fungal pathogen Sclerotinia sclerotiorum. Information on the genetic and molecular mechanisms governing trichome development in B. villosa is rare. Here, we analyzed an F2 population, derived from a cross between B. villosa and the glabrous B. oleracea by QTL mapping and transcriptomic analyses. As a result, the phenotyping of 171 F2 progenies revealed a wide range of variation in trichome development. Subsequent genotyping with the 15-k Illumina SNP array resulted in a genetic map with 970 markers and a total length of 812 cM. Four QTLs were identified, which explained phenotypic variation from 3.2% to 40.3%. Interestingly, one of these was partially co-localized with the major QTL for Sclerotinia-resistance previously detected in the same F2 population. However, only a moderate correlation between trichomes and Sclerotinia-resistance was observed. In total, 133 differentially expressed genes (DEGs) associated with trichome development were identified, from which only BoTRY, an orthologue of Arabidopsis TRY encoding a MYB transcription factor negatively regulating trichome development, was located within the major QTL. Expression of BoTRY was tissue-specific and highly variable between the hairy and glabrous species, suggesting that BoTRY may also act as a master-switch regulator of trichome development in B. villosa. This study provides valuable data for further understanding the genetic architecture of trichome development and identifying related genes and mechanisms in Brassica species. Molecular markers can be developed to facilitate the introgression and selection of this trait in oilseed rape breeding