Fully Funded PhD Student Position – RNA biology or mitochondrial function in oxygen sensing

The Max Delbrück Center for Molecular Medicine in the Helmholtz Association aims to transform tomorrow’s medicine through our discoveries of today. At locations in Berlin-Buch, Berlin-Mitte, Heidelberg and Mannheim, our researchers harness interdisciplinary collaboration to decipher the complexities of disease at the systems level – from molecules and cells to organs and the entire organism. Through academic, clinical, and industry partnerships, as well as global networks, we strive to translate biological discoveries into applications that enable the early detection of deviations from health, personalize treatment, and ultimately prevent disease. First founded in 1992, the Max Delbrück Center today inspires and nurtures a diverse talent pool of 1,800 people from over 70 countries. We are 90 percent funded by the German federal government and 10 percent by the state of Berlin.

Job Description

The Sugimoto Lab aims to elucidate how the human body and cells sense oxygen in health and disease. Our current research focuses on oxygen-dependent regulation of RNA by phase separation, and mitochondrial responses to hypoxia (a decrease in oxygen availability). We seek to understand fundamental mechanisms of human physiology, and to translate our findings to the treatment of diseases such as cancer, cardiovascular and neurodegenerative diseases, and developmental disorders. We are looking for a PhD student to extend our existing projects.

A fully funded PhD position is available in the Sugimoto lab. The student will work on one of the following two projects:

1. Oxygen-dependent regulation of phase separated molecular condensates.
Oxygen availability dynamically regulates diverse classes of phase-separated molecular condensates to control the fate of RNAs — including mRNA transcription, splicing, localisation, and translation. We recently discovered a set of oxygen-dependent post-translational modifications in RNA binding proteins that form molecular condensates, and a gene that catalyses these modifications. Building on these findings, the PhD project will elucidate how molecular condensates are regulated in accordance with oxygen availability, and/or how the dysregulation leads to diseases, including cancer, cardiovascular disease, and developmental disorders.

2. Mitochondrial responses to hypoxia
Evidence indicates that mitochondria respond rapidly to hypoxia, controlling systemic processes in the vasculature and respiration. On the other hand, mitochondrial defects are strongly associated with aging. We have identified a number of mitochondrial responses to changes in oxygen availability and related stresses (including mitochondrial morphology, activity, and autophagy). This project aims to elucidate the molecular mechanisms that confer oxygen sensitivity to mitochondria, and to explore approaches to intervene in the progression of aging processes.

For both projects, the PhD student will utilise the expertise of the Sugimoto Lab, including high-throughput DNA sequencing, mass spectrometry-based proteomics, single-cell and/or spatial multiomics, advanced imaging, iPS cells, machine learning, and computational biology.

The ideal candidate will have a passion for addressing fundamental questions in biology and an eagerness to learn/develop new techniques. The ability to work both independently and in a team is essential. The postholder will hold (or will shortly complete) a diploma/master degree in molecular, cell or computational biology. The postholder will have experience of basic molecular and cell biology techniques. Previous experience in RNA or mitochondrial biology is an advantage.

References:

• Sugimoto et al., Nature 2015 (PMID: 25799984)
• Cockman et. al., PNAS 2022 (PMID: 35930668)
• Sugimoto and Ratcliffe, Nat. Struct. Mol. Biol. 2022 (PMID: 36097292)
• Prange-Barczynska et. al., JCI 2024 (PMID: 39106106)

We offer

• International working environment with communication in English and German
• Interesting career opportunities and a range of opportunities for further qualification and training
• Compatibility of family and career certified by the workandfamily audit (“berufundfamilie audit”)
• Support for "New Berliners" through the MDC Welcome & Family Office

You also benefit from:

• A remuneration in accordance with the collective agreement for the federal public service (TVöD-Bund), including additional company pension schemes
• A vibrant and collaborative research environment
• Access to state-of-the-art technologies
• An idyllic green campus, which is easily accessible by bicycle, public transport or car
• On-campus health and fitness center, additional health benefits such as flu vaccination, eye test, ergonomics advice at the workplace
• On-campus nursery; nursery is free in Berlin
  (https://www.berlin.de/willkommenszentrum/en/families/day-care-centers/)

Please get in touch with any questions
Yoichiro Sugimoto
AG Sugimoto
yoichiro.sugimoto@mdc-berlin.de