Ruprecht-Karls-Universität Heidelberg
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Knop0219 - Scientist (f/m) / PhD position
Project no:
Knop0219

Project leader:

Project supervisor:
Knop, Michael
Application deadline:
31. May 2019
Start of PhD project:
1. Jul 2019

Project description:

Title:
Spatial proteomics of protein quality control in mammalian cells
Summary:
Protein homeostasis involves control over spatio-temporal distribution of each individual protein species inside a cell. To gain insight into the principles of protein function and the mechanisms underlying the control systems that regulate protein homeostasis, is essential to study protein dynamics and degradation with high resolution using endogenous expressed proteins.

In this project we will use our novel CRISPR/Cas12a based methods for the efficient endogenous gene tagging of protein in mammalian cells (Fueller et al., 2019, Buchmuller et al., 2019) to address key functions of proteins involved in protein homoestasis regulation. The PhD project will first establish high throughput imaging methods to analyse the expression and spatial distribution a selected range of proteins with respect to their function in membranous organelles, in particular the secretory pathway. Subsequent work will focus on a molecular mechanistic understanding of their functions.

The project will involve tissue culture work using mammalian cell lines, CRISPR/Cas genome engineering, high content microscopy and image analysis, nextGen sequencing-based methods for genotype analysis and various other cell biological techniques, mathematical modelling.

Work will be conducted in a small team of experienced researcher. We offer an interdisciplinary environment that allows a talented candidate to rapidly complement her/his skills and knowledge and to discuss solutions of upcoming challenges during the project.
References:
Buchmuller BC, Herbst K, Meurer M, Kirrmaier D, Sass E, Levy ED & Knop M (2018) Pooled clone collections by multiplexed CRISPR/Cas12a-assisted gene tagging in yeast. bioRxiv: 476804

Fueller J, Meurer M, Herbst K, Gubicza K, Kurtulmus B, Knopf JD, Kirrmaier D, Buchmuller BC, Pereira G, Lemberg MK & Knop M (2019) CRISPR/Cas12a-assisted PCR tagging of mammalian genes. biorxiv.org

Khmelinskii A, Blaszczak E, Pantazopoulou M, Fischer B, Omnus DJ, Le Dez G, Brossard A, Gunnarsson A, Barry JD, Meurer M, Kirrmaier D, Boone C, Huber W, Rabut G, Ljungdahl PO & Knop M (2014) Protein quality control at the inner nuclear membrane. Nature 516: 410–413
Methods that will be used:
Various tissue culture methods, high content microscopy, image data analysis and modelling of data, next Gen sequencing techniques and data analysis, statistical data analysis, various molecular biology techniques (oligoarrays, qPCR, standard cloning techniques, etc…).
Cooperation partners:
Björn Ommer – IWR
Marius Lemberg – ZMBH
Personal qualifications:
We are looking for outstanding candidates that combine excellent wet lab skills in molecular biology and tissue culture with theoretical and bioinformatics knowledge and very good computing skills (image analysis using ImageJ and Matlab, DNA sequence analysis and statistical bioinformatics using R and python). The candidate needs to be well organized and able to handle complex tasks.
Keywords: