Autophagy is most frequently assessed by analysis of the LC3 protein, which is a mammalian homologue of yeast Atg8 (“Autophagy-related gene 8”). Like Atg8 in yeast, LC3 is generally thought to be essential for autophagy in mammalian cells. In steep contrast to this view, we recently found that LC3 is not required at all for bulk autophagy in normal rat liver cells or in human prostate cancer cells (Szalai et al., 2015, Exp Cell Res 333, 21-38). Instead, we found that GABARAP proteins, which comprise another family of mammalian Atg8 homologues, were essential. This finding opens up a whole new and exciting avenue in the quest to understand central aspects of the autophagic process.
Project aims
The project aims to decipher the roles of individual Atg8 proteins in various cell types as well as in different types of autophagy. This will shed light on which Atg8 proteins are generally and fundamentally required for autophagy in mammalian cells, and which may have a more redundant or specialized function. Next, the project aims to understand some of the basic mechanistic aspects of how such essential Atg8 proteins work. The project will use state-of-the art techniques such as transfection with small-interfering RNAs, CRISPR-Cas9, mutagenesis and cloning, and a unique suite of assays to monitor autophagic activity.
Project-associated techniques
- Cell cuture
- Transient transfections with small-interfering RNA and expression plasmids
- CRISPR-Cas9 knock-out technology
- Mutagenesis and cloning
- RNA isolation, cDNA synthesis and real-time RT-PCR
- Western blotting
- Biochemical assays for the measurement of bulk autophagic sequestration and degradation activity
- Confocal fluorescence imaging, and imaging assays for selective types of autophagy
Expectations
You can expect a very exciting Master project, where you besides learning many useful techniques, will study central aspects of a truly fundamental cellular process (autophagy), and have the chance to make important novel discoveries at the fore-front of the field. You will be part of a focused team studying autophagy. We expect full-time commitment, scientific open-mindedness and curiosity, good communication skills, and a wish and ability to work independently under guidance.
Contact
If you are interested in this project, please contact Nikolai Engedal: k.n.engedal@ncmm.uio.no
or Oddmund Bakke, IBV – IBV 3rd floor oddmund.bakke@ibv.uio.no.