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Kaskadeneffekte anthropogener Störung auf die Aktivität von Wildhuftieren und die Baumverjüngung in einem urbanen Waldökosystem
Item type: Master Thesis
Gnägi, Johanna (2026)
Menschliche Störung kann in anthropogen geprägten Landschaften über Veränderungen im Verhalten von Wildhuftieren indirekt den Verbiss und damit die Baumverjüngung beeinflussen. Ziel dieser Arbeit war es, (1) die Einflussfaktoren auf die räumliche und zeitliche Aktivität von Reh (Capreolus capreolus) und Wildschwein (Sus scrofa) zu untersuchen, (2) die Einflussfaktoren auf Verbisshäufigkeit und -stärke zu analysieren und (3) Zusammenhänge zwischen anthropogener Störung, Wildtieraktivität und Verbiss zu prüfen, die auf Kaskadeneffekte hindeuten. Die Untersuchung wurde im Waldlabor Zürich durchgeführt, einem stark frequentierten, vom Menschen geprägten Wald. Die Aktivität von Wildtieren und Menschen wurde mittels Kamerafallen erfasst, während die Baumverjüngung im Feld mithilfe der k-Baum-Methode aufgenommen wurde. Die Auswertung erfolgte mit generalisierten linearen gemischten Modellen sowie Random Forest Modellen. Die Ergebnisse zeigen, dass Rehe und Wildschweine ihre Aktivität sowohl zeitlich als auch räumlich an anthropogene Störung anpassen. Rehe verlagern ihre Aktivität in die Dämmerung, Wildschweine in die Nacht, insbesondere im Winter und nutzen verstärkt Bereiche in grösserer Distanz zu Wegen. Verbiss wird vor allem durch Baumart, Höhenklasse und die Aktivität von Rehen beeinflusst, mit besonders hohen Verbissanteilen bei Eiche, Hainbuche und Kirsche, während ein Einfluss von Wildschweinen nur im Sommer nachweisbar war. Zudem zeigt sich, dass Verbiss im Winter von der Distanz zum Weg abhängt und in grösserer Entfernung zu Wegen häufiger auftritt. Damit wird deutlich, dass anthropogene Störung über Veränderungen in der Raumnutzung von Wildhuftieren mit dem Auftreten von Verbiss verknüpft ist und diese Zusammenhänge als verhaltensbasierte Kaskadeneffekte beschrieben werden können.
Applications of High-Resolution Mass Spectrometry in Metabolomics
Item type: Doctoral Thesis
Fido, Mateusz (2026)
Recent technological progress in the field of mass spectrometry has enabled it to become one of the most sought-after analytical techniques in contemporary biological research. Advancements in the construction of ionization sources, ion optics, and mass analyzers allow mass spectrometry to reliably detect masses of biomolecules with unparalleled accuracy and resolution. Multicomponent hybrid instruments are now able to combine the capabilities of several, previously separate machines. The advent of high-resolution mass analyzers has made it possible to study even the most challenging types of biological matrices, from complex biofluids to exhaled breath.
Of equal importance, advances in data acquisition methods and computational tools now allow more information to be extracted from any mass spectrometric measurement than ever before. Improved fragmentation methods and refined tandem mass spectrometry experiments now provide increased measurement certainty and give multifaceted insight into sample content. Data-dependent and data-independent acquisition methods ensure increased depth of coverage in complicated biological systems. Sophisticated deconvolution, integration, and peak-picking algorithms are able to construct a coherent, ever-clearer picture of the biology underlying metabolic interventions or disease states.
Together, these hardware and software developments have broadened the scope of mass spectrometry and its usecases. Large-scale multidisciplinary studies employing high-resolution mass spectrometry are becoming increasingly more common and are already a core part of many scientific fields. This cumulative thesis aims to showcase the different purposes which high-resolution mass spectrometry has in the study of metabolism, and how it can help answer major questions pertinent to biochemical processes that take place within an organism.
The first part covers a comprehensive analysis of materials used for preparation of containers applied in the collection and storage of gaseous samples (i.a., exhaled breath). There, high-resolution mass spectrometry has helped uncover previously unclear mechanisms of sample loss and degradation, and gave insight into the heterogeneity of contaminants emitted by the polymers.
The second work described the application of volatile metabolite analysis in the Western honey bee. By utilizing gnotobiotic animals we were able to uncover the dependence of the bee metabolome on their gut colonization status and the activity of their gut microbiota. Moreover, we were able to find volatile signatures of an opportunistic bacterial pathogen infecting bees, differentiated depending on their gut microbial status. Cross-validating with an established high-resolution mass spectrometry technique revealed complementary findings letting us build a global image of the bee's metabolic state.
In the third publication we presented a method based on high-resolution mass spectrometry hyphenated to liquid chromatography for precise detection and quantification of nitrogen-containing compounds, important not only from the standpoint of metabolomics but also microbial and environmental sciences. We applied the approach in several biologically relevant matrices to show its versatility and usefulness in multiple fields studying nitrogen metabolites.
Finally, we designed and implemented a computational tool for targeted analysis of high-resolution mass spectrometry data to facilitate tracing of multiple compounds with many representative masses. The application is open-source, available on all the major platforms, and allows the user to locally analyze and visualize complex mass spectrometry data without the need for long on-boarding necessary with commercial solutions.
In summary, these works provide an integrative view on the different aspects of high-resolution mass spectrometry in the context of metabolic research. Starting with ambient analysis of gaseous samples, through thorough method development and application in diverse biosystems, and finalizing with modern digital solutions for data analysis, they provide a detailed insight into the potential high-resolution mass spectrometry has and will continue to offer in biological sciences.
Environmental Humanities Switzerland ‐ a decade in retrospect
Item type: Journal Article
Kueffer, Christoph; Hall, Marcus; Forêt, Philippe C.; et al. (2025)
Environmental crises confront humanity with challenges that reach into all areas of society-from poverty and exclusion, capitalism and finance, to forced migration, global health, and artificial intelligence. This article traces the history of saguf's working group Environmental Humanities from 2014 to 2025 and reflects on its contributions in Switzerland and beyond.
Mechanics of thick-shell microcapsules made by microfluidics
Item type: Journal Article
Chen, Philipp W.; Brignoli, Jonathan; Studart, André R. (2014)
Double emulsion templates made by microfluidics allow for the production of tailored and monodisperse microcapsules. However, their mechanical properties cannot be predicted by traditional analytical models because of their relatively thick shells. In this work, we produce thick-shelled microcapsules with varying sizes and shell thicknesses and mechanically characterize them in single-capsule compression tests using Weibull statistics. We simulate their compression with finite element modeling and find a good agreement with the experimental results under linear elastic conditions, which enables the prediction of elastic properties based on bulk material parameters. Analysis of the simulated stresses show that capsules with a thickness-to-radius ratio above 20% consistently fail at a constant maximum principal stress in accordance with the brittle nature of their bulk material, enabling the extrapolation of their failure loads as well. Combining this structure-property correlation with processing-structure relationships found in previous studies provides a general predictive framework for the assembly of monodisperse microcapsules with tunable mechanics for protection and/or controlled release of encapsulants.
Agricultural diversification through the use of underutilized crops
Item type: Doctoral Thesis
Carmenati, Filippo (2026)
This thesis examines mixed cropping systems, focusing on their effects on co-growth dynamics (Chapter 2), post-harvest quality and nutritional stability (Chapter 3), and the provision of ecosystem services (Chapter 4), through comparisons between pure and mixed crop stands.
Growing interest in legumes as a source of plant protein and functional foods with high organoleptic value has increased across Europe. Consequently, the findings of this thesis are relevant for both the scientific community and the agri-food sector, providing empirical support for legume-cereal mixed cropping as a viable alternative to monoculture systems. Conducted within the framework of the European CROPDIVA project (September 2021 - August 2025), this thesis focuses on four underutilised crops: hull-less barley (Hordeum vulgare var. nudum), lentils (Lens culinaris), narrow-leaved lupin (Lupinus angustifolius) and buckwheat (Fagopyrum esculentum).
Despite their current limited cultivation, these species exhibit strong adaptive potential to climate change and possess high ecological and nutritional value, positioning them as promising candidates for integration into the agri-food sector’s ecological transition.
This study addresses two overarching research questions:
(i) Whether mixed cultivation of lentils and hull-less barley constitute a viable alternative to pure stands.
(ii) Whether the introduction of another crop into pure stands of lentils, narrow-leaved lupins, and buckwheat enhances the differentiation of regulatory and provisioning ecosystem services.
The first two studies of this thesis focus on lentil-hull-less barley systems. Chapter 2 investigates field-scale co-growth dynamics, identifying mixed cropping improve overall productivity. Compared with pure lentil stands, mixed cropping increased yield (+13%) and land use efficiency (+15%), while reducing weed biomass (−42%) and lodging (−36%). The yield gains were primarily driven by improved hull-less barley performance when grown in mixture with lentils, with increased tillering positively associated with the main production indices (LER and NE) and competitive dominance (CR). Mixed cropping also affected crop morphology and phenology, increasing barley tiller number and time to reach BBCH 55, and increasing lentils plant height by 11 cm.
Chapter 3 shows that improvements observed in the field were reflected in cereal quality traits. In mixed systems, the barley protein content increased by 1.8-2.6%, while no effects were found for lentils or barley beta-glucans, the latter increasing only under mineral fertilisation. Mixed systems also enhanced yield stability by combining barley’s responsiveness to favourable climatic conditions with the greater yield stability of lentils. In addition, seed size ratios were negatively correlated with harvest impurities, indicating that greater interspecific differences in seed size from the mixed harvest result in cleaner final products.
Finally, Chapter 4 demonstrates that the providing of ecosystem services is driven primarily by crop functional traits rather than by the cropping system itself.
Among the three crops studied, buckwheat emerged as the most multifunctional crop, while no significant differences were detected when crops between pure or mixed stands.
Overall, this thesis advances the understanding of mixed cropping systems, with particular emphasis lentil-barley associations, and provides agroecological insights linking field dynamics with post-harvest quality outcomes.