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Open Positions

Are you interested in more than one project?

Then you can specify up to 3 projects in your application.

Integration of a bacterial endosymbiont into the intracellular networks of a eukaryotic host cell (A01)

Angomonas deanei is a non-pathogenic trypanosomatid that contains a single proteobacterial endosymbiont. Intriguingly, cell cycles of host and endosymbiont are synchronized and the symbiont is tightly associated with several host cell glycosomes. Previously, we identified host proteins that apparently control the cell cycle of the endosymbiont. Furthermore, we found that a gene that was transferred from the endosymbiont to the host cell nucleus, encodes a metabolic enzyme that now localizes to the endosymbiont-associated glycosome, likely adjusting the metabolic capacity of the glycosome to the needs of the endosymbiont. Aims of the proposed project are (i) to explore host-symbiont metabolic integration with a special focus on the role of the glycosome in this process; (ii) to establish advanced optogenetic tools for A. deanei that will be instrumental in scrutiny of host-symbiont interactions; and finally, (iii) to establish a synthetic endosymbiosis system in mammalian cells that will allow us to study basic questions regarding host-symbiont interaction (e.g. by reconstructing processes such as nuclear control over endosymbiont division in an orthogonal system).

Project leaders: Eva Nowack, Matias Zurbriggen

Your tasks:

  • Investigation of the proteome composition of the A. deanei glycosome
  • Reconstruction of compartment-specific metabolic maps and characterization of the system by metabolomics (incl. isotopologue profiling)
  • Implementation of optogenetic tools (e.g. light-regulated gene expression systems) in A. deanei in close collaboration with the group of Matias Zurbriggen
  • Support of the Zurbriggen group in the establishment of synthetic endosymbioses using parts derived from A. deanei

Official job offer / Job advertisement (PDF)

Metabolic and Isotopologue profiling of intra and intercellular metabolic networks (Z02)

Metabolites are the key nodes of metabolic networks and can function as energy carrier, building blocks for biosynthesis and signalling molecules with regulatory functions. The homeostasis of metabolite pools and the dynamic of metabolite fluxes are essential for intracellular metabolism and also for complex interspecies microbial networking. In this facility, we will provide state of the art metabolomics approaches to the research groups of the CRC, using chromatography and mass spectrometry techniques. We will enable the researchers to perform metabolomics experiments to obtain metabolic profiles, monitor intracellular and extracellular metabolite pool sizes and measure fluxes via incorporation of stable isotopes.

Project leader: Philipp Westhoff

The future candidate will be the first point of contact for all research groups of the CRC regarding metabolite measurements and experimental design for metabolomics approaches. For broad metabolite coverage complementary chromatographic approaches such as RP-LC HILIC, anion exchange chromatography and gas chromatography will be used and further developed towards the needs of the CRC. The candidate will work with different mass spectrometry systems (QTOF, MSD, triple-Quad, Quad-Orbitrap) to perform targeted and untargeted assays to generate metabolic profiles, analyze signalling molecules and identify specific target molecules. Furthermore the candidate will support the researchers to perform stable isotope labelling assays and extract isotopologue information from mass spectra. In the CRC a variety of model organisms are used and therefore the candidate will support the researchers to develop and optimize harvesting, extraction and sample processing strategies to produce intra and extracellular metabolome samples for different species and experimental setups.

Official job offer / Job advertisement (PDF)

Integration of a bacterial endosymbiont into the intracellular networks of a eukaryotic host cell (A01)

Angomonas deanei is a non-pathogenic trypanosomatid that contains a single proteobacterial endosymbiont. Intriguingly, cell cycles of host and endosymbiont are synchronized and the symbiont is tightly associated with several host cell glycosomes. Previously, we identified host proteins that apparently control the cell cycle of the endosymbiont. Furthermore, we found that a gene that was transferred from the endosymbiont to the host cell nucleus, encodes a metabolic enzyme that now localizes to the endosymbiont-associated glycosome, likely adjusting the metabolic capacity of the glycosome to the needs of the endosymbiont. Aims of the proposed project are (i) to explore host-symbiont metabolic integration with a special focus on the role of the glycosome in this process; (ii) to establish advanced optogenetic tools for A. deanei that will be instrumental in scrutiny of host-symbiont interactions; and finally, (iii) to establish a synthetic endosymbiosis system in mammalian cells that will allow us to study basic questions regarding host-symbiont interaction (e.g. by reconstructing processes such as nuclear control over endosymbiont division in an orthogonal system).

Project leaders: Matias Zurbriggen, Eva Nowack

Your tasks:

  • Development, characterization and implementation of optogenetic tools (e.g. light-regulated gene expression systems, subcellular localization control) in animal cells and in A. deanei in close collaboration with the group of Eva Nowack
  • Establishment and characterization of synthetic endosymbiosis in mammalian cells.

Official job offer / Job advertisement (PDF)

 

 

Coupling of mitochondrial energy metabolism with microtubule-dependent mRNA logistics (A03)

Optogenetics relies on the engineering of microbial and plant photoreceptors to transduce information in the form of photons into a molecular function, mediated e.g. by a change in protein conformation or enzymatic activity, that is in turn used to control a wide range of cellular processes. In this project we will systematically design, engineer and implement light-sensitive switches for the spatiotemporal and quantitative control of mRNA and protein expression, stability and subcellular localization. In particular, we will apply the optogenetic tools in the fungus Ustilago maydis to study mRNA intracellular transport and mitochondrial function.

Project leaders: Matias Zurbriggen, Michael Feldbrügge

Your tasks:

  • Engineering, characterization and optimization of optogenetic tools for the light-regulated control of gene expression, mRNA and protein stability and subcellular localization in eukaryotes
  • Implementation of the optogenetic tools in U. maydis to study mRNA intracellular transport and mitochondrial metabolism and physiology in close collaboration with the Feldbrügge group

Official job offer / Job advertisement (PDF)

The role of carbohydrate-binding proteins and antimicrobial proteins (AMPs) in natural lichen and synthetic cross-kingdom communities (B02)

Lichens are among the most ancient and fascinating examples of complex microbial networking. In lichens, an algal or cyanobacterial photobiont tightly physically associates with a fungal mycobiont to establish an intimate mutualistic interaction. In this project, we will employ comparative genomics and transcriptomics to identify carbohydrate-binding proteins and antimicrobial proteins from a Peltigera mycobiont and uncover how they shape establishment and maintenance of a lichen community. Our approach will combine a biochemical and functional analysis of candidate proteins with their application in the establishment of a synthetic microbial consortium.

Project leaders: Florian Altegoer, Markus Pauly, Björn Usadel, Bart Thomma

The future candidate will investigate the Peltigera mycobiont secretome on the basis of a high-quality Peltigera rufescens reference genome provided by Björn Usadel sampled near Düsseldorf. A combination of structural modelling and sequence analysis will be used to generate a catalogue of antimicrobial, antifungal and other proteins with a potential influence on the lichen community. In close collaboration with Bart Thomma, these proteins will be expressed and purified by heterologous production in E. coli and P. pastoris followed by a comprehensive structure/function analysis. Production of interesting candidates will be established in U. maydis to understand the influence of these proteins in co-cultivation experiments in close collaboration with Kerstin Schipper. Furthermore, a surface display system for U. maydis will be developed to expose lichen carbohydrate binding proteins on the surface of U. maydis and together with Markus Pauly find out the key determinants that are needed to establish cell-cell contacts in a symbiotic interaction. This project combines computational approaches with biochemistry and cell biology to investigate the molecular repertoire of a cyanolichen community.

Official job offer / Job advertisement (PDF)

The role of carbohydrate-binding proteins and antimicrobial proteins (AMPs) in natural lichen and synthetic cross-kingdom communities (B04)

Phototrophic microorganisms such as green algae interact synergistically with heterotrophic bacteria and fungi in their environment. These organisms assemble into stable communities in the regions neighbouring unicellular algae, known as the phycosphere, and play roles in global carbon and energy cycles. However, the fundamental principles that govern phycosphere community assembly and dynamics are relatively poorly understood, particularly in terrestrial ecosystems. We aim to use the eukaryotic, photosynthetic model organism Chlamydomonas reinhardtii to build computationally designed, stable and robust synthetic consortia to establish a solid quantitative theory to explain fundamental principles governing microbial ecosystem establishment, dynamics and resilience.

Project leaders: Oliver Ebenhöh (HHU), Bart Thomma (Uoc), Ruben Garrido-Oter (MPIPZ)

The successful candidate will develop mathematical models to theoretically investigate of the dynamics of microbial communities. This work will be based at the Institute of Quantitative and Theoretical Biology at the Heinrich-Heine University Düsseldorf. A major goal of the project is to obtain a quantitative understanding how environmental factors determine the stability, resilience and diversity of a community. This requires to also understand the interaction mechanisms between species and how these lead to community properties, such as stability and resilience. For this, differential equations-based models will be developed. The initial approach will be based on extended MacArthur consumer-resource models, which describe ecosystem dynamics based on resource availability, metabolic competition and cross-feeding. During the course of the project, the models will evolve from abstract to highly quantitative and calibrated with experimental data. The models will be developed in direct collaboration with the experimental partners Ruben Garrido-Oter and Bart Thomma, who provide high-quality, time-resolved data on dynamic communities, and perform dedicated experiments to determine the metabolic functions of the community members. Model predictions will guide experimental design to challenge the model and optimise information gain.

Requirements: The successful candidate should have a strong mathematical background, experience with differential equations, some programming skills, and a keen interest in the biological questions addressed in this project. Moreover, good communication skills and enthusiasm for interdisciplinary exchanges are important.

Official job offer / Job advertisement (PDF)

The links between mitochondrial energy metabolism and intracellular stress response pathways (A04)

Cells respond dynamically and appropriately to various stress situations using a set of interconnected quality control pathways. For example, malfunctioning mitochondria are removed during stress conditions or nutrient limitation by mitophagy. The basis of this regulatory network governing the required adaptations as well as their hierarchy is largely unknown. The deubiquitinase complex Ubp3/Bre5 from S. cerevisiae is a key node linking a number of these quality control pathways. Here, we will apply in vivo and in vitro studies combined with synthetic switches and biosensors to decipher the molecular roles of Ubp3/Bre5 during intracellular stresses and altered mitochondrial energy metabolism.

Project leaders: Andreas Reichert, Lutz Schmitt

The future candidate will investigate the role of Ubp3/Bre5 in various stress response pathways including mitophagy in the model organism S. cerevisiae in the Reichert lab. This is a joint project between two labs (AG Schmitt and AG Reichert) and we all will work in a collaborative manner on this project. One student will focus on the in vitro and structural aspects (AG Schmitt) whereas the selected candidate will work on experiments using S. cerevisiae (AG Reichert). A number of standard genetic and biochemical techniques as well as advanced techniques such as proximity labelling proteomics, live-cell fluorescence microscopy, electron microscopy, metabolomics, cellular metabolic assays, RNA biology, and structural biology (cryo-EM and X-ray-crystallography) will we employed.

Official job offer / Job advertisement (PDF)

Role of ferritin-like proteins in the microbial iron metabolic network (A09)

Currently, we are looking for a PhD student (m/f/d) to further develop our multi-parametric image spectroscopy approaches to study the role of ferritin-like proteins for iron storage in cells. Our image spectroscopy approaches are based on STED microscopy and single molecule FRET measurements which enable quantification of molecular levels and their activity states in live cells. In this project, we will monitor ferritin-like proteins, which are an important storage of the trace element iron. Iron is essential for vital processes such as DNA biosynthesis or energy generation but iron also leads to radical formation and DNA damage when provided in excessive amounts. Here, we will develop tools to quantify the amount of ferritin-like proteins and iron in bacterial cells. We will compare different types of ferritins and show how intracellular iron pools are meticulously regulated to optimize bacterial growth and fitness. From our molecular sensitive image data we will eventually derive mechanistic models of the role of ferritin proteins for iron storage and availability.

Project leaders: Cornelia Monzel (HHU), Michael Bott (FZJ)

The candidate (m/f/d) will use biophysical and nanotechnological techniques, with focus on super-resolution microscopy and bioimage data analysis of single molecules. He/She will further develop employ nanotechnological approaches. The studies will be conducted within the framework of the CRC Microbial Networks at HHU and will be supported by project partners at HHU and the Research Centre Jülich. The applicant (m/f/d) is expected to have a master‘s degree in (bio-)physics, physical chemistry or nanotechnology and strong interest in interdisciplinary research. Experience in optical microscopy and image data analysis is preferred.

Official job offer / Job advertisement (PDF)

Race for iron: impact of siderophore- and heme-mediated networking on spatial interactions in defined microbial communities (B01)

The availability of iron significantly shapes microbial interactions. Iron is often a growth-limiting factor, due to the extremely low solubility of Fe3+ in aerobic and microaerobic environments. Hence, microbes employ various strategies to manage iron homeostasis, but little is known about the interactions on the dynamics and spatial development of microbial communities and the scales of iron-dependent microbial networking. In this project, we will assess competitive and cooperative strategies for the acquisition of iron in defined microbial communities involving microbial model organisms. This highly multidisciplinary project will enable us to observe microorganisms within their ‘race for iron’ for the first time.  Among a complementary portfolio of analysis tools, we will develop innovative microfluidic cultivation devices mimicking physically and chemically structured microenvironments and perform state-of-the art time-lapse microscopy and deep-learning image analysis.

Project leaders: Dietrich Kohlheyer, Julia Frunzke, Thomas Drepper

At the Forschungszentrum Jülich, the future candidate will develop and apply innovative microfluidic cultivation devices, in which we can accurately control the environment and tailor our microscopic ‘race for iron’ arena. By microfabrication techniques, cultivation cavities in the micrometer range will be fabricated enabling co-cultivations of different microorganisms. Additionally we intend to microstructure iron resources within these cultivation sites and implementing oxygen gradients at the same time. Automated time-lapse microscopy will be performed enabling spatio-temporally resolved analyses with highest single-cell resolution. Candidates should have a degree in Microsystems Engineering, Bioengineering, Mechanical Engineering or similar with a strong interest in interdisciplinary research. Ideally, you have experience in the fields of microfluidics, microscopy, microfabrication, microbiology, and image analysis.

 

Official job offer / Job advertisement (PDF)

The role of carbohydrate-binding proteins and antimicrobial proteins (AMPs) in natural lichen and synthetic cross-kingdom communities (B04)

Phototrophic microorganisms such as green algae interact synergistically with heterotrophic bacteria and fungi in their environment. These organisms assemble into stable communities in the regions neighbouring unicellular algae, known as the phycosphere, and play roles in global carbon and energy cycles. However, the fundamental principles that govern phycosphere community assembly and dynamics are relatively poorly understood, particularly in terrestrial ecosystems. We aim to use the eukaryotic, photosynthetic model organism Chlamydomonas reinhardtii to build computationally designed, stable and robust synthetic consortia to establish a solid quantitative theory to explain fundamental principles governing microbial ecosystem establishment, dynamics and resilience.

Project leaders: Bart Thomma (Uoc), Ruben Garrido-Oter (MPIPZ), Oliver Ebenhöh (HHU)

Antagonism within microbial interactions can be established through various mechanisms, including the exploitation of antimicrobials. The successful candidate will mainly work in the Thomma laboratory at the University of Cologne to test the stability and resilience of synthetic phototrophic microbial ecosystems, particularly associated with C. reinhardtii, by perturbation experiments based on invasion by competitor micro-organisms. To this end, we will exploit the soil-dwelling fungus Verticillium dahliae that has recently been shown to exploit antimicrobial proteins for selective microbiota manipulation and address the question what is the impact of fungal-derived antimicrobial proteins on C. reinhardtii and how this affected by phycosphere bacteria. The data generated from these experiments will be used to parametrise models that account for antagonistic interactions in the system together with the Doctoral Researcher in Mathematical Modelling.

Requirements: The successful candidate holds a master degree in biology or life sciences, with demonstrated experience in molecular biology and/or biochemistry, preferably in combination with microbiology, is creative, forward-looking, prepared to take responsibility, drive the research, and contribute novel ideas. Excellent oral and written communication skills in English are a prerequisite as well as enthusiasm for interdisciplinary research and collaboration.

Official job offer / Job advertisement (PDF)

Race for carbon: molecular carbon economics and logistics within a synthetic community (B03)

In natural habitats, microorganisms usually co-exist in highly complex communities, undertaking distinct roles, depending on the population density, the environmental conditions and resource availability. Yet, basic biochemical principles underlying these microbial consortia are still unknown. In a close collaboration with the experimental labs (Axmann and Schipper) we will study the formation of a synthetic community of the cyanobacterium Synechocystis and two fungi, Ustilago maydis and Saccharomyces cerevisiae. Microorganisms co-existing within the same niche are regularly switching between their nutrient strategies, often leading to a costly production of nutrients available not only to them, but also to their neighbours. In this project you will use computational modelling to increase our understanding of community dynamics and the role of key nutrients in its formation. We will expand on the assumption of the fundamental role of the competition for carbon in the assembly and stabilisation of the cross-kingdom community and investigate different carbon managing strategies between the consortia members, treating carbon either as a private or public good.

Project leaders: Anna Matuszyńska, Ilka Axmann, Kerstin Schipper

By applying an economics perspective on the microbial community, each community member can be classified as a public good producer, private-metabolizer or cheater (free-rider), depending on its metabolic, nutrient digestion strategy. In this project you will explore the role of public goods and strategies regarding carbon metabolism, economics and logistics in shaping community formation and dynamics. You will  conceptualize and build various mathematical models, based on population dynamics and evolutionary game theory, and learn how to integrate data from multiple sources. Iterative mathematical modelling will be tightly integrated with experimental approaches, hence genuine interest in the biological question is essential. This project requires strong background in mathematics, physics or quantitative biology. Good programming skills, ideally in Python, are necessary prerequisite to take this project. The position is offered in the group of Matuszyńska at RWTH Aachen.

Official job offer

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