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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 - Nils-Alexander Lakomek

One PhD position is available in Biophysics / NMR spectroscopy at Forschungszentrum Jülich in the lab of Nils-Alexander Lakomek.

As part of the CoViPa consortium, the Bartenschlager, Sachse and Lakomek labs aim at an improved understanding of host determinants of SARS-CoV-2 replication to identify common pathways as targets for broad-spectrum antiviral therapy. As part of that approach they aim at the atomic structural characterization of key viral host complexes, with the focus on replication organelle (RO) formation. In particular the Sars-CoV-2 non-structural proteins nsp3 and nsp4 involved in double membrane vesicle (DMV) formation will be investigated at atomic resolution in an integrated cryo-EM and NMR approach.

Here, the Lakomek group will focus on the conformational dynamics and dynamic binding interactions of nsp3 and nsp4, investigated by a combination of solution and solid-state NMR spectroscopy. The PhD project will involve the application and development of novel proton-detected solid-state NMR experiments at very fast magic angle spinning (MAS) frequencies. Therefore, a strong background in physics, biophysics or physical chemistry is required. If you are interested in joining a dynamic and inter-disciplinary team working at the interface of physics and structural biology, please have a closer look at this website.

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

Subproject 3 - Andrea Kröger, Ana Zenclussen

Within Subproject 3, headed by Dunja Bruder (HZI), Andrea Kröger (HZI) and Ana Zenclussen (UFZ) we aim to understand how SARS-CoV-2 overcomes natural barriers to enter the host, particularly concentrating on the mechanisms involved in the upper and lower respiratory tract and at the feto-maternal interface.

We are looking for 2 motivated PhD students. Candidates have completed university studies (master or diploma) with strong immunological background. Experience in animal experiments or a background in virology is an advantage. The candidates will work in close cooperation with some experiments jointly performed in Braunschweig or Leipzig.

Student 1 (enrolled at HZI, Braunschweig) will perform in vivo/ex vivo SARS-CoV-2 infection studies to gain fundamental insights in innate immune response to the virus in the upper versus lower respiratory tract and to uncover long-term effects of preceding SARS-CoV-2 infection on host immunity to secondary triggers. These studies will require experimentation under biosafety level (BSL) 3 conditions. Student 1 will also be involved in behavior experiments using SARS-CoV-2 infected offspring.

Student 2 (UFZ, Leipzig): will carry out the experiments aimed to understand the interaction of viruses with trophoblasts among others. Additionally, to understand whether intrauterine vertical transmission takes place, SARS-CoV-2 infections under BSL 3 conditions are necessary, this will be conducted at the HZI in Braunschweig.

Subproject 3

Subproject 4 - Chris Lauber, Stefan Seitz

2 OPEN PhD POSITIONS in the field of virus bioinformatics (Hannover & Heidelberg)

We are a highly complementary research team located at the TWINCORE Centre for Experimental and Clinical Infection Research in Hannover (Chris Lauber) and the German Cancer Research Center in Heidelberg (Stefan Seitz). Our work is dedicated to the large-scale discovery and evolutionary analysis of novel viruses by high-throughput screening of Next-Generation sequencing data. To this end we established and applied sensitive computational pipelines that allowed us to retrieve thousands of genomes of so far unknown eukaryotic viruses. The current project aims at assessing the spillover risk of these infectious agents from non-human host reservoirs into mankind and thus contributes to fostering our preparedness against future pandemics.

This project is embedded in the interdisciplinary, multicenter Corona Virus Pathogenesis (CoViPa) consortium funded by the Helmholtz Society. The two open PhD positions include participation in a joint Graduate program to support highly talented and promising students at the early stages of their career.

To join our research team, we are seeking for highly motivated candidates holding a Master's degree in (bio)informatics or biotechnology with a focus on computational biology. Desired qualifications are:

  • Strong hands-on experience in programming with at least one scripting language, like Perl, Python or R, under Linux.
  • Knowledge in and understanding of state-of-the-art methods of computational biology, e.g. NGS data processing, sequence alignment, phylogenetic tree reconstructions, protein functional annotation, motif search and structural predictions.
  • Experience with high-performance computing is a plus.
  • Experience with tools for workflow management (e.g. Snakemake, Nextflow) and version control (e.g. git) is a plus.
  • Prior 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 and is willing to advise students in the lab.
  • Fluency in English language (written and spoken) is mandatory. Proficiency in German would be a plus.

References:

  • Lauber et al. 2017. Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses. Cell Host Microbe. 22:387-399.
  • Lauber et al. 2019. Discovery of Highly Divergent Lineages of Plant-Associated Astro-Like Viruses Sheds Light on the Emergence of Potyviruses. Virus Res. 260:38-48.
  • Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The Species Severe Acute Respiratory Syndrome-Related Coronavirus: Classifying 2019-nCoV and Naming It SARS-CoV-2. Nat Microbiol. (2020) 5(4):536-544.
  • Lauber et al. 2013. The footprint of genome architecture in the largest genome expansion in RNA viruses. PLoS Pathog 9(7): e1003500.

Subproject 4

Synergy Group 2 - Andreas Pichlmair

One postdoctoral researcher position is available at the Technical University of Munich (TUM) in the lab of Andreas Pichlmair: "Multi level omics analysis of virus infections"

The pathogenic activity of viruses is to a large extent based on their ability to modulate protein activities in infected cells. We generate omics data (interactome, effectome, transcriptome, proteome, phosohoproteome, ubiquitinome) to understand basic principles of virus-host interactions to deduce functional relevant interactions that can be potentially exploited for antiviral therapies. (www.innatelab.org)

We aim to bridge the information on cellular effects and signaling events gathered by proteomics analysis with single cell RNAseq data in order to deduce signaling events operative at single cell resolution. You will generate novel omics datasets and/or perform computational analysis of data from virus-perturbed cells. We aim to perform medium throughput functional screens based on automated live-microscopy, FACS, mass spectrometry or deep sequencing to validate the analysed data and to illuminate the virus-host interface on a functional level.

You should have profound knowledge in virology and virus-host interactions and/or bioinformatics analysis of complex datasets. You will closely collaborate with wet-lab or bioinformatics scientists: from the initial experiment design to the hypothesis validation. Your creativity and critical input will be a key driver in these projects.

Synergy Group 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

Synergy Group 3 - Robert Thimme, Maike Hofmann

At TEXIMMED2-FR (Translational EXperimental IMmunology lab MED II, University Hospital Freiburg) we seek a motivated

PhD student

Project: SARS-CoV-2-specific CD8+ T cell immunity in natural infection and after vaccination
(SARS-CoV-2 vaccines: a balance between protection and immunopathology)

Your assignments:

You will perform the analyses of CD8+ T cell responses during the natural course of SARS-CoV-2 infection and after vaccination strategies. This includes but is not limited to

  • autonomous processing of research tasks dealing with immune responses in viral infections
  • strong collaborative work within the CoViPa consortium
  • application of state-of-the-art and cutting-edge methods of cell and molecular biology including high dimensional FACS, single cell transcriptome analysis and CyTOF
  • establishing of new methods to elaborate on subsequent research questions
  • presentation of results on regular lab and consortium meetings and international conferences
  • writing of manuscripts for publication in international peer-reviewed journals

Prerequisites:

  • graduation (M. Sc.) in biology, molecular medicine or related subjects preferentially with focus on immunology or virology
  • strong interest in translational research and immunological research questions
  • distinct working autonomy combined with a high capacity for teamwork
  • a careful and focussed working habit
  • pleasure in scientific working and documentation

https://www.uniklinik-freiburg.de/medizin2/forschung/experimentelle-forschung/ag-thimmehofmann.html 

Synergy Group 3

2 MD Students per year: Further information on request

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