Vacancies

The PERICO research programme aims to uncover how a central metabolic organelle, the peroxisome, participates in controlling cellular metabolism. Metabolism and metabolic control are emerging as important frontiers in physiology. This is because, in our rapidly changing world, we face the effects of both metabolic extremes – from obesity on the one hand to malnutrition on the other. Learning how to control energy metabolism is therefore one of the most pressing challenges of the 21stcentury.

Peroxisomes are key metabolic organelles, which must communicate and interact extensively with their environment to exchange metabolites and coordinate cellular responses. Membrane contact sites (MCS), where membranes of two organelles are physically tethered to enable rapid transfer of small molecules, enable organelle communication and are crucial for coordination of cellular functions and hence human health. Research on organelle interactions and communication is a challenging, upcoming field in current cell biology.

PERICO will exploit recent developments in high-throughput and genome-wide screening technologies, combine these with modern molecular cell biology and systems biology and ultimately translate the data into new leads for drug discovery and therapy.

Early Stage Researchers

The training schemes include specific research projects, secondments to partner organizations, a wide range of dedicated courses, and workshops organized by the academic and industrial partners of the Network. The scientific training programme will be complemented with training in managerial soft skills.

The positions for Early Stage Researchers are available for candidates with a research experience ≤ 4 years (counted from the diploma that gives the rights to embark in a doctoral degree).

Candidates must not have resided or carried out their main activity (work, studies, etc) in the country of their host organisation for more than 12 months in the 3 years immediately prior to recruitment (short stays, such as holidays, are not taken into account).

Requirements

Candidates should have:

  • exceptional academic performance, including qualifications, prizes
  • subject specific skills and expertise (see project descriptions)
  • communication, presentation skills and team working abilities
  • competence in written and spoken English.

Length of appointment: 3 years
Type of contract: temporary

Starting date: April 1, 2019

Applicants can apply for multiple positions.

More information on the project

Descriptions of the individual PhD projects

Reference: ESR3-NL

A PhD position is available at the University Medical Centre Groningen, Department Paediatrics, Centre for Liver, Digestive and Metabolic Diseases, The Netherlands.
Project title: Translational models for peroxisomal dysfunction in genetic disease and malnutrition
Description:
In this ‘Systems Medicine’ project we will focus on the construction of computational models to understand how severe acute malnutrition (SAM) leads to sustained dysfunction of peroxisomal and mitochondrial metabolism. A challenge for such an approach is to bridge the gap between computational models and the in vivo metabolism in patient tissues. To this end the PhD student will also develop in vitro disease models, such as liver organoids and iPS-derived liver cell culture. Tasks include:

  • Establish an in vitro model for SAM (liver iPS cells and/or organoids in medium deprived of amino acids).
  • Biochemical characterization of the in vitro malnutrition model, focusing on fluxomics and proteomics.
  • Construct a computational model of the interplay between peroxisomes and mitochondria in lipid metabolism.
  • Model-informed interventions to rescue peroxisomal-mitochondrial function.

Location: Groningen, The Netherlands
Supervisor: Prof. Dr. B.M. Bakker (b.m.bakker01AT umcg.nl)
Co-supervisors: Prof. Dr. V. Martins Dos Santos, Lifeglimmer GmbH & Dr. R. Bandsma, The Hospital for Sick Children
Planned secondments: The Hospital for Sick Children, KU Leuven, Lifeglimmer GmbH
Required subject specific skills and expertise: A masters’ degree in life sciences, biophysics, biochemistry, or a related field, with clear affinity for metabolism and mathematics.
Application deadline: 27/01/2019
Starting date:  April 1, 2019

Application form ESR3

Reference: ESR5-NL

A PhD position is available at Lambert Instruments, Groningen, The Netherlands
Project title: Autonomous High-Throughput accurate FLIM with subcellular resolution
Description:
Development and optimization of automated data mining from multi-well microscopy plates.
The goal is to improve on current intensity-based methods for detection of the presence of biological phenomena in microscopic images by applying deep-learning for morphological analysis in detection and classification. Additional discriminating dimensions are created by integrating Fluorescence Lifetime Imaging Microscopy (FLIM) measurements into the dataset. The end point is a fully automated processing workflow to detect subtle changes in organelle morphology. The research involves improvement of a FLIM protocol for speed and accuracy, optimize modulation and illumination parameters, develop noise reduction algorithms. By using active feedback loops for real-time measurement adjustment, the harvest of target patterns will be optimized using reinforcement learning or other control algorithms for digital microscopes.

Location: Groningen, The Netherlands
Supervisor: Prof. Dr. L.R.B. Schomaker (l.r.b.schomakerATrug.nl); Mr. J. Wehmeijer (jeroenATlambertinstruments.com)
Co-supervisors: Prof. Dr. I.J. van der Klei, University of Groningen & Prof. Dr. M. Fransen, KU Leuven
Planned secondments: KU Leuven, University of Groningen
Required subject specific skills and expertise: a master’s degree in computer science or artificial intelligence with specialisation in image processing and (deep) machine learning. Experience with biological imaging techniques is advantageous but not mandatory.
Application deadline: 27/01/2019
Starting date:  April 1, 2019

Application form ESR5

Reference: ESR8-DE

A PhD position is available at the University of Freiburg, Department of Biochemistry & Functional Proteomics, Freiburg, Germany
Project title: Dynamics and regulation of ER-peroxisome contact sites
Description:

  • Mapping of in vivo phosphorylation sites in Pex30p-dependent ER-peroxisome contact sites (EPCONS) under different conditions in yeast using high-resolution mass spectrometry.
  • Identification of kinases mediating phosphorylation events and their preferred target sites to decipher the cellular signalling pathway(s) regulating EPCON formation.
  • Functional analysis of EPCONS using site mutants of selected proteins mimicking or preventing phosphorylation or targeting selected protein kinases and signalling pathways using conditional mutant strains or specific kinase inhibitors.
  • Characterizing human PEX30 and its role for the formation of EPCONS.

Location: Freiburg, Germany
Supervisor: Prof. Dr. B. Warscheid (bettina.warscheidATbiologie.uni-freiburg.de)
Co-supervisors: Prof. Dr. L.R.B. Schomaker, Lambert Instruments & Prof. Dr. I.J. van der Klei, University of Groningen
Planned secondments: University of Exeter, Lambert Instruments, University of Groningen
Required subject specific skills and expertise: a master’s degree in biology, biochemistry or a related discipline. Experience in proteomics/mass spectrometry and molecular genetics is advantageous but not mandatory.
Application deadline: 27/1/2019
Starting date:  April 1, 2019

Application form ESR8

Reference: ESR9-DE

A PhD position is available at the University of Freiburg, Department of Biochemistry & Functional Proteomics, Freiburg, Germany
Project title: High-resolution proteomics of peroxisome-centred membrane contact site (MCS) and transporters
Description:

  • Definition of the peroxisomal membrane proteome of yeast, human/mammalian cells, and trypanosomes using high-resolution quantitative mass spectrometry (MS) to identify putative new transporters.
  • Screen for novel membrane contact site (MCS) proteins in yeast using artificial protein tethers, quantitative MS, and computational data analysis.
  • Interactomics and proximity proteomic studies of key proteins forming MCS in different organisms and/or under different growth conditions.
  • Global loss-of-function studies of peroxisome-deficient yeast cells and cells with non-functional MCS and transporters and analysis of the cellular response to the lack of peroxisomes and impaired MCS/transporters by quantitative MS-based proteome studies.
  • Computation of an MCS interaction and cellular response network integrating the results obtained and published data (icw LG).
  • Computational integration of proteomics, lipidomics and metabolomics data from peroxisome-deficient cells and cells with non-functional MCS/transporters (icw LG).

Location: Freiburg, Germany
Supervisor: Prof. Dr. B. Warscheid (bettina.warscheidATbiologie.uni-freiburg.de)
Co-supervisors: Prof. Dr. V. Martins dos Santos, Lifeglimmer GmbH & Prof. Dr. M. Schuldiner, Weizmann Institute of Science
Planned secondments: University of Groningen, Weizmann Institute of Science. Lifeglimmer GmbH
Required subject specific skills and expertise: a master’s degree in biology, biochemistry or a related discipline. Experience in proteomics/mass spectrometry and a strong interest in bioinformatics are advantageous but not mandatory.
Application deadline: 27/1/2017
Starting date:  April 1, 2019

Application form ESR9

Reference: ESR10-DE

Are you fascinated by biology and bioinformatics in a dynamic company setting? A PhD position is available at the Data Analytics company Lifeglimmer GmbH, Berlin, Germany.
Project title: Model-driven discovery and network modelling of peroxisomal interactions
Description:

  • To identify novel transporter proteins using whole genome searches, analysis of protein sequences of newly identified proteins by bioinformatics tools, including structure prediction.
  • Carry out bioinformatics analysis for domains/transmembrane regions rational design of proteins in yeast
  • Define flux distributions and phenotypes in altered growth/beta oxidation capacity through metabolomics and modelling (mammalian/human cells)
  • Unravel peroxisomal crosstalk by systems biology approaches
  • Semantically integrate heterogeneous datasets

Location: Berlin, Germany
Supervisor: Prof. Dr. V. Martins dos Santos (vdsATlifeglimmer.com)
Co-supervisors: Prof. Dr. B.M.  Bakker, University Medical Center Groningen & Prof. Dr. B. Warscheid, University of Freiburg
Planned secondments: KU LEUVEN, University Medical Center Groningen, University of Freiburg
Required subject specific skills and expertise:

  • Master degree or equivalent in Computational Biology, Bioinformatics,  Systems Biology, Bio(techno)logy or related field;
  • Solid knowledge of bioinformatics;
  • Basic knowledge in (genome-scale) metabolic modelling;
  • Good understanding of molecular biology/biochemistry;
  • Experience in pathway analyses and/or omics data integration would be of advantage;
  • Experience in analysing omics data as well as interpretation of their biological implications;
  • Basic knowledge of common methods of functional genomics;
  • Experience in discussing results of computational analyses in collaboration with wet-lab scientists;
  • Good programming skills in R (Matlab) and experience in at least one other programming language (Python, Perl, Java, C++);
  • Knowledge of semantic web technologies (XML, RDF, SPARQL) would be an asset;
  • A pragmatic and solution oriented working style;
  • Enthusiasm for communicating with various project partners;

Application deadline: 17/02/2019
Starting date:  April 1, 2019

Application form ESR10

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