Cell Physiology and Applications
Below, you can find the updated list of Bachelor and Master internships available at the moment.
For more information on available internships on Single-cell Physiology and on Host microbiome interactions, please contact directly the teamleaders in this group:
Jurgen Haanstra – j.r.haanstra[at]vu[dot]nl
Herwig Bachmann – h.bachmann@vu.nl
Remco Kort – r.kort@vu.nl
| Project title | Type of research | Supervisor(s) |
|---|---|---|
| 1. Accessory functions in the pangenome of the human vaginal commensal Lactobacillus crispatus 2. Bacterial strain engraftment in the gorilla gut microbiome after fecal transplantation | Two Internships Bioinformatics (Master) | Dr Douwe Molenaar Prof Remco Kort (r.kort@vu.nl) |
| 1. The accessory genome in bacteria can be considered the cradle for adaptive evolution. For this internship a set of whole genome sequences of L. crispatus will be analyzed and accessory functions in the pangenome will be evaluated with a particular emphasis on functions that are important for sustained colonization in the host. Techniques: differential analysis of a large set of sequenced genomes. Duration: 6 months Further reading: van der Veer C, Hertzberger RY, Bruisten SM, Tytgat HLP, Swanenburg J, de Kat Angelino-Bart A, Schuren F, Molenaar D, Reid G, de Vries H, Kort R. (2019) Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota. Microbiome 7:49. Hertzberger R, May A, Kramer G, van Vondelen I, Molenaar D, Kort R (2022) Genetic elements orchestrating Lactobacillus crispatus glycogen metabolism in the vagina. Int J Mol Sci. 23:5590. 2. A fecal transplantation has been carried out to cure Akili, the ARTIS silverback gorilla, by recovery of the gut microbiota after antibiotic treatment. Longitudinal 16S rRNA profiling and metagenome data have been collected in donor and recipient feces to monitor bacterial population dynamics in the gut before, during and after the fecal transplantation intervention. The data will be analyzed with particular emphasis on bacterial strain engraftment. techniques: comparative metagenome analysis (optional metabolic analysis) duration: 4-6 months Further reading: Houtkamp IM, van Zijll Langhout M, Bessem M, Pirovano W, Kort R. (2023) Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity. Gut Microbiome. 4:e12 |
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| Metabolism in health and disease | Experimental or computational (combinations are possible) Bachelor/master | Jurgen Haanstra |
| The work in this topic aims to understanding control and regulation of metabolism to reveal selective drug targets in pathogens and other disease-causing cells. In addition, we also want to understand these aspects for healthy cells to make sure that interventions against the disease will not harm them. We work with the parasite Trypanosoma brucei and with liver cancer cells in the wetlab, but also do research on the parasite Schistosoma mansoni, on head- and neck cancer and blood cell precursors in the dry-lab (always in collaboration with experimental labs Techniques: Wetlab: cell culture, metabolite measurements, enzyme assays. Dry lab: kinetic modelling (COPASI, PySCes (python-based), genome-scale modelling |
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| Developing and optimizing a glycolytic sensor toolbox | Experimental (Master) | Dennis Botman d.botman@vu.nl |
| Glycolysis is a central metabolic pathway in many organisms, playing a crucial role in energy production and cellular function. It is particularly significant in rapidly proliferating cells, such as cancer cells. Therefore, there is a growing need for sensors capable of accurately measuring key intracellular metabolites and parameters involved in glycolysis, such as pH, NAD, glucose, fructose-1,6-bisphosphate (FbP), and pyruvate. Biosensors based on fluorescent proteins offer a promising approach, but existing options often suffer from limitations such as low brightness or sensitivity to pH changes. To address these challenges, you will help with developing and optimizing novel biosensors in various spectral colours for glycolytic metabolites. Once validated as robust tools, these sensors will enable us to gain deeper insights into glycolytic processes in both healthy and diseased states. | ||
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