|
Project properties |
|
| Title | Function & Mechanism of Prokaryotic Immune Systems |
| Group | Biochemistry, Laboratory of |
| Project type | thesis |
| Credits | 24-36 |
| Supervisor(s) | Depends on project |
| Examiner(s) | Daan C. Swarts |
| Contact info | daan.swarts@wur.nl |
| Begin date | 2023/02/01 |
| End date | 2026/01/01 |
| Description |
Prokaryotes have evolved a diverse arsenal of immune systems that provide protection against the constant threat of invading nucleic acids such as viruses and plasmids. In the last decade, numerous different prokaryotic immune systems (e.g. CRISPR-Cas and prokaryotic Argonaute proteins) have been characterized. Both CRISPR-Cas and Argonaute systems use small nucleic-acid guides that allow for sequence-specific recognition of target DNA. These prokaryotic immune systems are not only interesting from fundamental biology and evolutionary biology perspectives, but their utilization as programmable genome editing tools or nucleic acid detection tools caused a revolution in basic biology research. Furthermore, these tools have a great potential for diagnostic purposes and to treat genetic diseases in the future. Although certain prokaryotic immune systems are well studied, there is tremendous diversity, and most systems remain poorly characterized. We are interested in the diversity of prokaryotic immune systems from a fundamental perspective, and additionally are interested in the possibilities of repurposing them as molecular tools. We have different rapidly developing projects running at the same time. If you are interested in the research in our group, please contact Daan Swarts (daan.swarts@wur.nl) to get more information on available projects! Also take a look at www.swartslab.org for more information! Please note we get more requests for BSc thesis projects than we can offer places. If you are looking for a BSc thesis spot in our group, it is advisable to contact us as early as possible. |
| Used skills | A project can comprise one or more of the following techniques (can be agreed upon between student/supervisor depending on requirements of projects and desires of student)
DNA cloning PCR, (HiFi) cloning, E. coli transformation, sequencing, etc Bacterial genetics/microbiology techniques Generating knock-in/knock-out strains (i.e. genomic mutants), phenotype analysis, full-genome sequencing, in vivo protein characterization, microscopy, proteomics, transcriptomics, metabolomics, (usually with E. coli or T. thermophilus), etc Proteins expression and purification Heterologous (over)expression, affinity purification of tagged proteins, FPLC, SDS-PAGE, pull-down and Mass-Spectrometry, etc In vitro protein characterization Nuclease assays, High-throughput fluorescence-based assays, Fluorescence polarization assays, SEC-MALS, Pull-downs, etc Structural biology Structural modelling (e.g. AlphaFold), Far-UV Circular Dichroism, X-ray crystallography, Structure analysis, Molecular Dynamics simulations, etc |
| Requirements | Background in protein biochemistry, for most projects ideally the student has experience in protein purification (e.g. BIC20806) |