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Research project (§ 26 & § 27)
Duration : 2021-06-01 - 2022-05-31

Strain and process improvement is one of the most labour-intensive and time-consuming phases of biotechnology process development. High-throughput screening is usually in miniaturized static cultures which compromises scalability, so that further intermediate screening steps are needed. Maturing of existing technology to deal with additional cell culture types (i.e. mammalian cells) and incorporate further analytical developments to support metabolite and product screening requirements are identified as the key steps to creating a technology of commercial value. In this project, we propose to mature an existing µ-screening platform with two major pillars addressing these steps. Firstly, extending the applicability of the module to fermentation technology based on Chinese Hamster Ovary (CHO) cultures. Secondly, to expand the analytical value of the platform using a combination of valve technology and mass spectrometry to develop a fully integrated platform suitable for application in biotechnology facilities.
Research project (§ 26 & § 27)
Duration : 2020-11-01 - 2023-02-28

The combination of ion mobility-mass spectrometry (IM-MS) with separation techniques such as liquid chromatography (LC) is now emerging as a powerful platform for addressing the identity confirmation of unknown organic compounds within complex samples. Electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) are two widespread ion sources for IM-MS, in which the mechanism of ionization is based on protonation/deprotonation of the analyte or cation/anion attachment. Studying these phenomena theoretically alongside experimental confirmation on a commercially available instrument is recognized as a key aspect of addressing the broad analysis of unknown compounds via untargeted workflows, where several 1000 molecular features are typically resolved within a single LC-IM-MS analysis. In an IM-MS platform equipped with APCI or ESI ion sources, the formation of the product ions and consequently the sensitivity of IM-MS to a given analyte, M, depends on the nature of M, the source conditions applied, and solvents during ionization processes. As such, establishing an improved knowledge about the ion/molecule reactions occurring in the ionization region of an IM-MS, potential conformations of ionic species, the nature of the ion/molecule interactions, and the parameters influencing these interactions enables analytical chemists to modify the existing analytical techniques to improve their detection limits and sensitivities, provide better characterization of unknown molecules, and/or to avoid some interferences that reduce the analytical performance.
Research project (§ 26 & § 27)
Duration : 2020-09-01 - 2023-08-31

Reducing herbicide use is an important social and environmental goal, as concern is growing about the development of herbicide-resistant weeds and the ecological consequences of herbicide application. Several cover crops are known to successfully suppress weeds, providing a pertinent answer to this problem. However, in order to use cover crops adequately, the mechanisms of weed suppression need to be elucidated and understood. Besides direct resource competition, growth repression through root interactions can play a decisive role. However, so far rhizosphere interactions of two neighboring plants have received little attention in the scientific community. In previous experiments we could demonstrate that below ground interactions between the cover crops Fagopyrum esculentum (buckwheat) and Avena strigosa (black oat) led to growth suppression of Amaranthus retroflexus (redroot pigweed), presumably induced by specific cover crop root exudates. Based on these findings, we aim to further investigate cover crop root exudates and to identify putative growth suppressive compounds. We will test six research hypotheses: (H1) The selected cover crops can recognize the presence of heterospecific neighbors via interacting root systems, which leads to a systemic modification of cover crop root exudation. (H2) Certain compound groups and/or specific molecules respond to a species-specific recognition, while others respond more generally to the presence of another plant. (H3) Certain compound groups and/or specific molecules from cover crop root exudates are responsible for growth suppressive effects. (H4) Growth suppressive effects are reflected by transcriptome changes of Arabidopsis thaliana (thale cress) and Brachypodium distachyum (stiff brome). (H5) Arabidopsis thaliana and Brachypodium distachyum root exudation is altered by the presence of different cover crops. (H6) Putative compounds responsible for growth repression can be detected in agricultural soil. Our methodological approach employs a validated split-root set-up enabling differential root exudate collection and analysis. First experiments will be performed in undisturbed soil-free glass bead cultures. Differential chemical analysis of the collected exudates will follow an already implemented workflow utilizing accurate mass spectrometry in combination with fit-for-purpose separation methods. Identity confirmation of significant compounds will make use of dedicated accurate mass databases including information on fragment spectra. Subsequently, root exudates will be collected from soil grown roots and rhizosphere soil solution to confirm their presence in soil. Moreover, phenotypic and transcriptomic changes induced by direct interaction of roots and the impact of selected compounds will be studied in Arabidopsis thaliana and Brachypodium distachyum. The results of the studies will provide novel insights in belowground plant-plant interactions and provide information for the development and use of weed suppressive cover crops, as a step towards new cultural control strategies for integrated weed management.

Supervised Theses and Dissertations