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Please send your applications to covipa-bw@dkfz-heidelberg.de 

Subproject 2 - Carsten Sachse

Two PhD positions are available in cryo-EM image processing at the ERC-3 in the field of structural biology of the Forschungszentrum Jülich in the lab of Carsten Sachse.

The candidates will work on critical virus-host interactions that most likely account for the direct cytopathogenic effect of SARS-CoV-2 and other coronaviruses. As our main tool we will employ advanced imaging methods, including cryo-EM, correlative light and electron microscopy/tomography (CLEM), live cell imaging and super-resolution microscopy as well as associated image processing.

1. The successful candidate should have a master degree in bioinformatics, biophysics or related field. The candidate will be using and developing cryo-EM image processing methods to determine the 3D structures of biological macromolecules. We expect to use novel imaging approaches and apply computational methods of pattern recognition, artificial intelligence and deep learning to improve 3D reconstruction and density map interpretation methods. Familiarity with the Unix operating system is required and prior knowledge in programming will be a plus.

2. The successful candidate should have a master degree in biochemistry/cell biology, biophysics or related field. The candidate will be working on high-resolution cryo-EM structure determination of in situ cellular samples using correlative light and electron microscopy approaches.

Subproject 2

Subproject 2 - Ralf Bartenschlager

OPEN POSITION for a postdoctoral fellow / doctoral student in the research group of Ralf Bartenschlager

The Bartenschlager group is studying the interaction between plus-strand RNA viruses and their host cells. One major focus is the 3D architecture, biogenesis and molecular composition of the membranous replication organelles of hepatitis C virus, flaviviruses (dengue virus, Zika virus) and SARS-CoV-2. We use standard molecular and cell biological methods, -omics based approaches (proteomics, lipidomics), genetic screening as well as cutting-edge light and electron microscopy methods (e.g. Cortese et al., 2020; Cerikan et al., 2020; Romero-Brey et al., 2012; Welsch et al., 2009). To complement our research team and to work on the SARS-CoV-2 replication organelle, we are seeking for a highly motivated postdoctoral fellow / PhD student. Desired qualifications are:

  • A Ph.D. / Master's (or equivalent degree) in biology or related field with an excellent publication record.
  • Strong hands-on experience with cryo-EM, conventional EM and light microscopy.
  • Solid experience in state-of-the-art cell and molecular biology techniques.
  • Profound knowledge in cell biology.
  • Sound knowledge in virology is of advantage.
  • The candidate works accurately, is able to conduct independent research, but also enjoys working in an international and interdisciplinary environment. The candidate is willing to advise students in the lab.
  • Good presentation skills and experience on project management (importance of scheduling, deliverables, reporting) will be highly valued.
  • Fluency in English language (written and spoken) is mandatory. Proficiency in German would be a plus.

Further information about our research can be found at:
https://www.klinikum.uni-heidelberg.de/Molecular-Virology.104862.0.html

References:

  • Cortese et al., 2020. Integrative imaging reveals SARS-CoV-2 induced reshaping of subcellular morphologies. Cell Host & Microbe 28(6):853-866.e5.
  • Cerikan et al., 2020. A Non-Replicative Role of the 3' Terminal Sequence of the Dengue Virus Genome in Membranous Replication Organelle Formation. Cell Reports 7;32(1):107859.
  • Romero-Brey et al., 2012. Three-dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication. PLoS Pathog. 8(12):e1003056.
  • Welsch et al., 2009. Composition and three-dimensional architecture of the dengue virus replication and assembly sites. Cell Host Microbe 5:365-75.

Subproject 2

Synergy Group 2 - Herbert Schiller

A position for a postdoctoral fellow is available from 1st of August in the Schiller lab at Helmholtz Zentrum München.
The postdoctoral fellow in the Schiller lab will set up and run several ex-vivo and in-vitro models of human lung, including air-liquid interface culture of primary airway and alveolar epithelial cells, precision cut lung slice cultures, and alveolar organoids. These models will be subjected to virus infections and highly multiplexed biological perturbations (e.g. small molecules targeting pathways, cytokines) coupled to single cell transcriptomic readouts and other omics measurements (see figure below). The postdoc will work in close collaboration with the labs of Prof. Andreas Pichlmair (TUM) and Prof. Fabian Theis (HMGU, ICB) as part of a Synergy group embedded in the CoViPa consortium (Project 'Functional multi-omics analysis of antiviral immunity and interactions of pandemic viruses with primary human lung tissue´). Virus-induced pathology originates from molecular and cellular interactions, which are initiated by the virus in the host tissue. In this project we will combine the (1) virus & proteomics expertise of the Pichlmair laboratory (TUM) with the (2) single cell genomics and lung pathology expertise of the Schiller laboratory (HMGU) and (3) the integrative computational analysis of the Theis laboratories (HMGU) in order to generate pipelines that characterize virus-host interactions in complex tissues. In a data-driven approach we aim at identifying key regulators of antiviral immunity and immunopathology, which will be functionally evaluated. We anticipate that this approach will pinpoint options for antiviral therapies.


The Helmholtz Zentrum München (HMGU; https://www.helmholtz-muenchen.de) - a research institution within the Helmholtz Association of German Research Centers, is a leading center in health research with a focus on Environmental Health. The Comprehensive Pneumology Center (CPC, www.cpc-munich.org) at HMGU is a translational research center dedicated to respiratory medicine, which is also a partner site of the German Center for Lung Research (DZL; www.dzl.de), an association of the leading university and non-university institutions dedicated to lung research in Germany.


Twitter: @SchillerLab

Google scholar: https://scholar.google.com/citations?hl=en&user=XZt2fpYAAAAJ

Pubmed: https://pubmed.ncbi.nlm.nih.gov/?term=schiller+hb&sort=date

Recent relevant work of the lab:

• Muus C, Luecken MD, et al. Nat Med. 2021 Mar;27(3):546-559. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
• Mayr CH, .... , Schiller HB. EMBO Mol Med. 2021 Apr 9;13(4):e12871. Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
• Strunz M, ...., Schiller HB. Nat Commun. 2020 Jul 16;11(1):3559. Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis.
• Ziegler CGK et al. Cell. 2020 May 28;181(5):1016-1035.e19. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.
• Schiller HB, ..., Nawijn M. Am J Respir Cell Mol Biol. 2019, Jul;61(1):31-41. The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.
• Angelidis I, ..., Schiller HB. Nat Commun. 2019 Feb 27;10(1):963. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics.

Your responsibilities
• Establish and maintain ex vivo models of human lung (organoids, ALI culture and precision cut lung slices)
• Multiplexed single cell multi-omics method development and testing in human organotypic models
• Establish and use multiplexed single molecule FISH / spatial transcriptomics in the ex vivo models
• Integrative bioinformatic analysis of the single cell perturbation omics data from the organotypic models
• Confocal and light sheet microscopy and image analysis

Your qualification
• PhD degree in biology or related area
• Previous experience with single cell genomics and systems biology
• Previous experience with lung and ex vivo / in vitro models
• Passion for science, innovation and creative and independent work
• Proficient in written and spoken English

Our offer:
• Working in an innovative, well-equipped and scientifically stimulating environment
• Training and supervision in cutting edge technologies (single cell genomics, spatial omics, computational biology, imaging techniques)
• Team member in Human Cell Atlas consortium working on the Lung
• Initial employment contract for 2 years with a standard public service salary (TV-ÖD E13)

Synergy Group 2

2 MD Students per year: Further information on request

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