The Konstanz Research School Chemical Biology invites applications for Fellowships for PhD Students from highly motivated and enthusiastic students with a keen interest in interdisciplinary research and with an excellent degree (Master or Diploma) in Biology, Chemistry, Computational Life Science, or related areas.

The current call offers stipends financed by our graduate school with the starting date 1 October 2015, as well as stipends financed by the German Academic Exchange Service (DAAD) with individual starting dates in 2016.

Notification of the success of the application will be not before 1 September.

Application Procedure: Our next call is open from 4 June till 16 July 2015!

Position 1: Michael Berthold – Bioinformatics and Information Mining

Guiding Analytics in Life Science

This project focuses on the new area of Guided Analytics, with a particular emphasis on applications in the life sciences. In close cooperation with colleagues in the graduate school Chemical Biology, a framework will be developed that formalizes mechanisms to deploy complex analyical workflows to experimental scientists at various levels of abstractions. The project encompasses both theoretical aspects (framework formalization, categorization of extisting work) and practical work (prototypes for colleagues in the life science domain). In addition to collaborations within the University, the project is also tied to the newly established BMBF Bioinformatics Infrastructure project and in particular to our partners at University of Tübingen and FU Berlin.

The project can be funded either by a fellowship or by a position.

Position 2: Alexander Bürkle – Molecular Toxicology & Karin Hauser – Biophysical Chemistry

Combining Biochemical and Biophysical Approaches to study Non-Covalent Poly(ADP-ribose) – Protein Interactions

Poly(ADP-ribosyl)ation is a eukaryotic post-translational protein modification catalyzed by poly(ADPribose) polymerases (PARPs) with implications in many cellular functions including chromatin remodeling and cellular stress response mechanisms. Apart from covalent modification of protein with PAR at specific amino acids, PAR can interact with proteins in a non-covalent manner via specific PAR binding sites. Our previous studies have shown that this non-covalent interaction regulates macromolecular complex formation and protein functionality. This project is located at the interface of biology (Bürkle lab) and chemistry (Hauser lab). The aim of this project is to dissect the biochemical and biophysical basis and consequences of the non-covalent PAR-protein interactions using state of the art methodology, such as static and time-resolved infrared spectroscopy and a wide spectrum of biochemical methods. In conclusion, it is expected that this approach gives molecular insights into the mechanisms of how poly(ADP-ribosyl)ation regulates physicochemical properties of target proteins. We are looking for a candidate with a strong background and interest in biochemistry and chemical biology.

The project can be funded by a fellowship.

Position 3: Elke Deuerling – Molecular Microbiology

Molecular Mechanisms of Cellular Aging

The molecular mechanisms of aging are manifold and still poorly understood. Protein synthesis by ribosomes is a central pathway for the renewal of the proteome and thus believed to be a major determinant for cellular youthfulness and vitality. In this project we will use C. elegans as animal model to study the consequences of aging on the molecular level in Metzoans. C. elegans is perfectly suited as the population of these animals can by synchronized starting at an early larvael stage and cellular changes can be monitored at different ages of the population. A particular focus will be put on understanding the age-related changes of ribosomes and protein synthesis.

The project is funded by a position at the Deuerling group.

Position 4: Daniel Legler – Immunology and Cell Biology

Role of Receptor Glycosylation in Controlling Receptor Homeostasis and Cell Migration

Cell migration along chemokine gradients is pivotal not only for the induction of adaptive immunity, but also for metastasis formation. In this collaborative project between the Legler (immunology and cell biology) and Wittmann (organic and bioorganic chemistry) groups, we aim to investigate how glycosylation of chemokine receptors is shaping chemotactic responses using chemical, biochemical, cell-biological and immunological tools.

The project is funded by a fellowship.

Position 5: Michael Pester – Microbial Ecology and Limnology

Pyrite Formation from FeS and H2S – a Novel Energy Metabolism

The reaction of iron sulfide (FeS) and hydrogen sulfide to yield pyrite (FeS2) plus hydrogen has been discussed as one of the first forms of energy metabolism on Earth and is also known as one of the Wächershäuser reactions. Until today, this process is massively occurring in marine and freshwater sediments being an important part of the global iron and sulfur cycle but so far has not been linked to biological activity. Microbial enrichment cultures, which have been established from marine and freshwater sediments, perform this reaction in conjunction with a methanogenic partner. This project aims to elucidate the identity of the involved microorganisms as well as the reaction mechanisms and th einvolved metabolic pathway by a combination of genomics, proteomics, and single-cell Raman-microscopy. 

This project is funded by a fellowship.

Position 6: Marina Rubini – Organic Chemistry and Cellular Chemistry

Co- and Post-Translational Engineering of Erythropoietin with Non-Natural Amino Acids

The therapeutic glycoprotein Erythropoietin (EPO) plays a crucial role in the treatment of different types of anemia and is one of the best-selling therapeutic proteins worldwide. Within this project several recombinant EPO variants containing different non-natural amino acids will be created to provide orthogonal sites for the chemo-selective conjugation of cabrohydrate or PEG moieties by different ligation methods. The goal is to increase our mechanistic understanding of protein-glycan interactions and the potential of PEGylation versus glycosylation for the development of robust EPO variants with improved therapeutic properties. The suitable candidate should have a strong background in Molecular Biology and Biochemistry. A moderate interest for Organic Chemistry would also be appreciated.

THe project is funded by a fellowship.

Position 7: Dieter Spiteller – Chemical Ecology and Chemical Biology

How do Actinomyces Coordinate Secondary Metabolite Production in Response to their Environment?

Actinomyces bacteria are invaluable due to their highly diverse secondary metabolites. Many of which are used in medicine, e.g. as antibiotics. From genome sequencing it became evident that Actinomyces possess many more gene clusters for secondary metabolite production than products have been identified from them. Under usual laboratory conditions Actinomyces obviously have no need to produce all these compounds whereas under particular conditions it can be expected that most of these compounds are produced in response to certain environmental challenges.

This project aims to reveal how Actinomyces react to environmental factors, e.g. heavy metal ion stress or cocultivation with other organisms. Using differential metabolite profiling the differences in secondary metabolim between varying growth conditions will be revealed. Induced secondary metabolites will be identified using a combination of mass spetrometry, NMR and genome mining. The biological function of identified metabolites will be studied in appropriate bioassays. In addition, the pharmaceutical value of newly identified compounds will be investigated. Moreover, the molecular basis of factors leading to the induced production of secondary metabolites should be addressed.

We will follow an interdisciplinary approach combining techniques of microbiology, genome mining and analytical chemistry, Therefore, a stron interest and background in natural products chemistry, analytical chemistry (mass spectrometry and NMR) and/or genome mining is required.

The project is funded by a fellowship.

Position 8: Florian Stengel – Cellular Proteostasis and Mass Spectrometry

The Global Interaction Landscape of Macromolecular Machines involved in Proteostasis

While recent years have greatly heightened our understanding of the architecture and function of protein complexes that are involved in homeostasis as static entities, our knowledge of how these intact molecular machines are allocated within a cell and interact with each other to keep-up proteome maintenance, is scarce. Here, a single high-resolution structural approach is unlikely to succeed. Rather, the combination and integration of multiple hybrid methods will be needed to interprete such complex macromolecular assemblies.
For this project, mass spectrometry, structural proteomics and computational modeling will be integrated with more traditional biochemical approaches. This hybrid approach will be used to monitor the architecture and dynamics of large macromolecular assemblies and their influence on homeostasis globally on the level if the intact protein complex.

Candidates should have a solid training in molecular biology, biochemistry or life science. An interest in computational work and modeling would be an advantage and script writing skills a plus.

This project is funded by a position at the Stengel group.

Position 9: Florian Stengel – Cellular Proteostasis and Mass Spectrometry & Andreas Marx – Organic and Cellular Chemistry

Synthesis and Application of Novel Cross-Linkers for the Analysis of Proteasomal Assemblies

One of the main advantages of using MS approaches for addressing protein-protein interactions on a structural level is the relative ease and speed with which results can be attained for a large number of proteins. One important and particular promising approach for achieving this goal is chemical crosslinking coupled to mass spectrometry. We aim at expanding the structural mass spectrometry toolbox by synthesizing novel bi- and trifunctional cross-linking reagents for the quantitative and dynamical structural probing of intact protein complexes in their cellular environment (i) and to attain information on protein-RNA/DNA complexes (ii) and protein-lipid (iii) interactions by mass spectrometry.

Candidates should have a solid training in chemistry, biochemistry or life science and should be eager to combine organic chemistry with mass spectrometry.

This project is funded by a fellowship.

Position 10: Valentin Wittmann – Organic and Bioorganic Chemistry

Design, Synthesis, and Evaluation of Shiga Toxin Inhibitors

Shiga toxins are the key virulence factors expressed by several enterohemorrhagic strains of E. coli (EHEC). They belong to the clinically relevant AB5 toxins consisting of a toxic A subunit that gains entry to susceptible mammalian cells after oligosaccharide recognition by the five identical B subunits that assemble into a pentagon-shaped structure. High-affinity ligands that can neutralize Shiga toxins are of great medical interest. Based on our expertise in the development and investigation of multivalent ligends, this project aims at the design and synthesis of multivalent Shiga toxin ligands. Newly developed ligands will be thoroughly investigated by different binding and inhibition assays. Furthermore, X-ray crystallography will be employed to characterize the interaction of the synthesized ligands with the B5 subunit of the toxin that will enable us to further improve the structure of the ligands.

Eligibility

To qualify for admission, you should hold a master’s degree (or equivalent) in Biology, Chemistry, Life Science, or related subjects. You should have finished your studies significantly above average, and have a proven interest in chemical biology.

Students who have already started PhD work at the University of Konstanz can also apply within the first year of their studies.

Application Projects

How to Apply

Four steps to your application: REGISTER › LOG IN › UPLOAD › SUBMIT

1) REGISTER with our online application platform. Once you registered you will receive a confirmation email to install your personal account.

2) LOG IN to work on your application, please fill in your contact data and provide the following:

A maximum of three PhD projects you are interested in, chosen from the list of projects and ranked by your preference

A motivation letter (max. 500 words)

Contact details for two academic references (please note that we will contact them during the application process ourself)

State where the call came first to your attention.

3) UPLOAD the following documents (in English or German):

Curriculum vitae (only accepted in chronological order)

Copy of your bachelor’s and master’s degree certificates (or equivalent) incl. transcripts of records

Proven proficiency in English: at least level B2 of the Common European Framework of Reference for Languages is required (Here you can find detailed information on acccepted certificates).

4) SUBMIT your application until 16 July 2015 at the latest!

Applications are only accepted via our online application platform (https://korscb.glowbase.com/login)

Admission Timelines

  Starting Date:

 1 April

 1 October

  Call for Applications

  December / January

  June / July

  Deadline CfA

  15 January

  16 July

  Decision Board Meeting

  End of February

  End of August

  Notification until

  1 March

  1 September

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