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Teaching at the University of Bonn

• PFLS: Python for Life Scientists (Master) (GitHub repository)
• BIO-13: Physiologie und Molekularbiologie der Pflanzen (Bachelor)
• WBIO-A-07: Analyse biologischer Daten mit Python (Bachelor)
• WBIO-A-08: Bioinformatik in den Pflanzenwissenschaften (Bachelor)
• iGEM (optional: 2025/2026)
• Research modules, Bachelor theses, and Master thesis can be conducted in our group. Please find additional details here.

Open Projects for Students:

Characterizing New Genes

• Content: DNA extraction, PCR, molecular cloning, and transformation of plasmids into bacteria, followed by transformation into mutant A. thaliana plants. Testing the phenotype of the transformed plants to see if their mutation has been complemented.
• Background: Newly discovered genes from different species might not always correspond to the functions predicted by their functional annotations. For some gene functions, this complementation assay is a solid method to assess gene function. We are especially interested in structural and regulatory genes from the anthocyanin and general flavonoid biosynthesis pathways.

Lentibulariaceae Project Topics

Lentibulariaceae is a family of carnivorous plants. Interestingly, all three genera - Pinguicula, Genlisea, and Utricularia - have different mechanisms for catching prey, making them particularly interesting from an evolutionary perspective. What traits are shared among the different genera? Which traits are specific to the Lentibulariaceae? Which of these traits could potentially contribute to the evolution of carnivorous characteristics in plants? How can we utilize Lentibulariaceae?

• Content: Extracting DNA from plants in the Lentibulariaceae family. Optimizing and conducting PCR for specific genetic regions. After Sanger sequencing of these amplified regions, the sequences will be analyzed and compared to determine the species of the plants.
• Background: Genotyping is important for classifying unknown plant material for further genomic studies.

Bacterial Cloning of a New Plasmid into Agrobacterium tumefaciens

• Content: PCR and cloning of a new, pre-planned plasmid. First into Escherichia coli, followed by plasmid extraction and transfer into A. tumefaciens. Final evaluation will be conducted through full plasmid sequencing.
• Background: The plasmid will be used to transform Utricularia and will contain a new construct with two different fluorescent proteins.

Optimization of Utricularia neglecta in vitro Culture with Plant Hormones

• Content: Working with in vitro plant cultures, making regular subcultures, preparing different media, and testing them. Observing the resulting plant growth.
• Background: Our current in vitro cultures utilize BAP (6-Benzylaminopurine) as a plant hormone to induce the growth of meristem tissue. This is the fastest method we have achieved for growing high biomass of U. gibba. Unfortunately, this does not work as well for our U. neglecta cultures. The idea is to adjust the concentration of the hormone or to test other hormones to determine which conditions are better suited for this plant species. U. neglecta cultures are of interest because they have larger traps than U. gibba. Generally, in vitro cultures are used to transform the plants.

Bioinformatics: Analyzing U. neglecta Flowers

• Content: Analyzing transcriptomic data from different flower tissues of U. neglecta using bioinformatics tools (e.g., Kallisto, DESeq2) to identify differentially expressed genes among the various tissues. With the help of robust functional annotations, biosynthetic pathways and their transcriptional regulation can be investigated.
• Background: The stems of the flowers are red, and the yellow flowers themselves have some red lines. It is interesting to discover which pathways are responsible for the different colors and how they are regulated. This could later be compared to other Lentibulariaceae.

Bioinformatics: Genomic Analysis of U. neglecta

• Content: Conducting genomic and comparative genomic analyses, such as synteny analysis of genomic regions containing interesting genes like various proteases. This analysis can be expanded to include a wide variety of other interesting genes. Additional analyses may involve determining the number of possible duplications of the genes of interest (GOIs) and further investigations, including phylogenetic tree construction, prediction of gene product localization, promoter and transcription factor binding site prediction, and comparison of GOIs on a molecular level.
• Background: Searching for potentially carnivory-related genes and investigating their prevalence across Lentibulariaceae can help us better understand the specific evolution of this family. One potential GOI could be directly linked to carnivory (a protease that is putatively duplicated in higher numbers in the Lentibulariaceae than in other plants).

Transformation of Utricularia

• Content: Handling in vitro cultures of Utricularia plants. Growing Agrobacteria and co-culturing them with in vitro plants under different conditions. Regenerating plants from transformed cells.
• Background: To genetically modify the genome of a plant, the Agrobacterium tumefaciens-mediated transformation method is widely used. This method has already been applied to Utricularia gibba by other research groups. We aim to establish this method in our lab as well, to investigate trap-related transport mechanisms.

If you are interesting in working in one of these projects, please have a look at our contact page to get in contact.

Previous Courses at TU Braunschweig

• MB09: Introduction to Biochemistry and Bioinformatics of Plants
• GE37/BB35: Data Literacy and Genome Research
• BB34: Python for Life Scientists
• GE33: Applied Plant Transcriptomics
• 1399100: 'Recent developments in molecular plant biology and bioinformatics' (seminar)
• LMChemBSc-12: Biochemistry and molecular biology of plants for food chemists
• 1399430 (DaLiP): Data Literacy in Genomics (for Bachelor students)
• 1399440 (DaLiP): Data Literacy in Genome Research (for Master students)
• GE31: Applied Genome Research
• GE32: Data Literacy in Plant Sciences

 
Data Literacy in Plant Genomics (DaLiP)

This project is a teaching innovation that was funded by "Stiftung Innovation in der Hochschullehre" as part of "Freiraum2022".

Course content and concept: Using the example of a plant genome sequencing, the students should plan and practically carry out all work steps of a real project. One focus here is on the integrated teaching of content from different subjects, including biochemistry, molecular biology, genomics and bioinformatics. The project begins with compliance with legal requirements such as the Nagoya Protocol when selecting samples. In addition, the students learn how to combine information from various sources in order to optimally plan their project. They will then plan their work steps in the laboratory to extract high molecular weight DNA and perform sequencing using nanopore technology (MinION). A particular challenge is the efficient utilization of the sequencing capacities. The students assume responsibility for valuable equipment and materials. Molecular biology laboratories and equipment are provided by the Plant Biotechnology and Bioinformatics group. All work steps are documented by the students in a digital laboratory book. The students should mutually review their documentation and make suggestions for improvements (peer review). This sharpens the understanding of important details in the metadata through cooperative learning. I have already had good experiences with digital laboratory notebooks and peer review for protocol control in a project funded by the Stifterverband. Another innovative element of this project is the presentation of progress via social media. The aim is to acquire initial skills for science communication. The planned sequencing will generate large datasets, so students will gain experience in handling large datasets. These data sets are to be processed, whereby an exact documentation of all steps is essential. A cloud-based solution is to be used for the analyzes in order to show current developments in bioinformatics. The students learn to find reliable backup solutions in order to avoid the loss of data sets. Finally, the final datasets are to be published via the established repositories. This includes the European Nucleotide Archive for the sequencing data. A precise description of the sequencing process is necessary. In this context, the students should internalize the concept of FAIR (Findable Accessible Interoperable Reuseable) data. Different options for the publication of datasets should be compared by the students with regard to their advantages and disadvantages. At the end of the event, the students should present their results to an international audience in a self-organized online conference.

 Learning objectives:Students should be able to independently plan, implement and fully document data-intensive projects (data literacy); plan and carry out genome sequencing projects and other omics projects independently; analyze large datasets cloud-based and publish their results; present their work and its results to an interested public and a specialist audience.

'digi fellowship'

The Stifterverband awarded me a teaching fellowship for digital innovation in higher education. My project at Bielefeld University was about a digital lab book to document methods and results of a practical course in molecular biology. Evaluation of this documentation was based on peer feedback. Please get in touch if you are interested in my experiences.

Previous Courses at Bielefeld University

• Applied Python Programming for Life Scientists
• Applied Genome Research
• Molecular Methods in Genome Research

My teaching materials are shared to support open education. Feel free to re-use my materials/courses shared on GitHub.