DynaMem Vacancies and Application

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DynaMem Vacancies

Ready to qualify for a PhD in an interdisciplinary research project? You are an enthusiastic and highly self-motivated team player? 13 PhD positions are offered by the LOEWE core area DynaMem "Dynamics of Membranes: Molecular Basics and Theoretical Description" or short “DynaMem". DynaMem is an interdisciplinary research program combining labs from the faculties of physics, biochemistry, chemistry and pharmacy, biosciences, and medicine. Two to three labs will work together on one of the 10 cooperative projects of DynaMem leading to a broader knowledge of membrane dynamics finally to allow the prediction of the dynamic behavior of membranes and the impact of membrane manipulation. Vacancies are available at the Goethe University Frankfurt am Main, the Goethe University Hospital Frankfurt am Main, the Johannes Gutenberg-Universität Mainz, the Max-Planck-Institute for Biophysics Frankfurt am Main, and the Frankfurt Institute of Advanced Studies. The salary of all vacant positions is according to 65 %-E13 TV-H (Frankfurt), or TV-L (Mainz) respectively. Contracts should start around 1st of April 2018.

Individual Research Projects available.


Projects in Manipulation of membrane functions


     1. Function of membrance active proteins in bacteria
     group of Helge Bode, Goethe University Frankfurt am Main. 
     more details

     2. Function of membrance active proteins in bacteria 
     group of Nadja Hellmann, Johannes Gutenberg-University Mainz, Germany.
     more details

     3. Function of membrance active proteins in bacteria
     group of Ute Hellmich, Johannes Gutenberg-University Mainz, Germany.
     more details

      4. Targeted manipulation of membrane dynamics by synthetic molecules
     group of Heinz D. Osiewacz, Goethe University Frankfurt am Main, Germany.
     more details

     5. Targeted modulation of membrane dynamics via small molecules.
     group of Dirk Schneider, Johannes Gutenberg-University Mainz, Germany
     more details

     6. Membrane dynamics by vectorial lipid organization
     group of Robert Tampé, Goethe University Frankfurt am Main, Germany.
     more details

     7. Tailor-made synthetic molecules for directed membrane perturbation
     group of Ralph Wieneke, Goethe Universität Frankfurt am Main, Germany.
     more details


Projects in Cellular Modelling of membrance dynamics


     8. Membrane dynamics and its role in pathogenesis of multiple myeloma.
     group of Ivan Dikic, Goethe University Frankfurt am Main, Germany.
     more details

     9. Characterization of FGF-induced FGFR-receptor oligomerization by NMR and advanced
     light microscopy

     group of Harald Schwalbe, Goethe University Frankfurt am Main, Germany.
     more details

     10. Manipulation of mitochondrial properties by altering the mitochondrial fatty acid
     synthase (FAS)

     group of Martin Grininger, Goethe University Frankfurt am Main, Germany.
     more details


Projects in Dynamics of membrane systems and organelles


     12. Dynamics of organelles and organelle surrounding membranes
     group of Enrico Schleiff, Goethe University Frankfurt am Main, Germany.
     more details

     13. Quantitative Dynamic Light Sheet Fluorescence Microscopy
     group of Ernst Stelzer, Goethe University Frankfurt am Main, Germany.
     more details

     14. Data analysis and modeling for spatio-temporal dynamics of cell-cell interactions
     group of Franziska Matthäus, Goethe University Frankfurt am Main, Germany.
     more details


Successful applicants will be employed: 42 months. The salary orientates on E13 T-H or T-L (65 %). The net salary results from deducting all compulsory (employer/employee) social security contributions, as well as direct taxes (e.g. income tax), and insurances from the gross amounts according to the regulations of the host country.

How to apply

Applications shall be addressed directly to the the project manager Bernd Märtens (b.maertens@em.uni-frankfurt.de) and sent via email (PDF-files). Deadline for applications is the 15th of January 2018. For applying please send us

- the project(s) name(s) you are applying for

- an application letter.

- your CV,

- a copy of your certificates (from Bachelor on), a copy of Master or Diploma, Bachelor, including accredited transcript of records (Master, Bachelor - including information on the Grade Point Average of the highest university degree obtained)

- a motivation letter (not more than 1 page)

- reference contact data

- a list of publications (if available)

- and further documents required to demonstrate your experience (if applicable)

- a priority list in case you are intend to apply for more than one project.


Research projects

Projects in Manipulation of membrane functions

Project 1-3: Function of membrance active preoteins in bacteria: : from origins to applications

The work groups of Helge Bode (Molecular Biotechnology, Goethe University Frankfurt), Nadja Hellmann (Inst. Biochemistry, Gutenberg University Mainz) and Ute Hellmich (Inst Biochemistry, Gutenberg University Mainz) are looking for

3 PhD students (E13/65%), starting April 1st 2018. The positions will be filled for 3.5 yrs (as a qualification position to obtain a PhD).

Every year, tens of thousands of people suffer from pathogenic bacteria or famine due to crop parasite/insect infestations. Therefore, safe, cheap and effective antibiotics but also anti-insecticides are urgently needed. Conveniently, soil bacteria that use insects as their food source, do not just scavenge dead insects but also synthesize a large repertoire of yet unclassified compounds that kill insects efficiently and protect the insect cadaver against food competitors like other bacteria (acting as antibiotics). These compounds include, but are not limited to, peptides including lipopeptides.

In a collaborative effort, the Bode, Hellmann and Hellmich groups want to characterize these compounds, focusing on the aforementioned (lipo)peptides, with regards to their lipid-interactions, ability to alter membrane properties and ultimately to use them as a tool in anti-insecticides.

The successful candidates will work closely together to identify novel (lipo)peptides which are involved in enabling bacterial and nematode survival, to determine their mode of action, to identify proteins involved in transport of these (lipo)peptides and the host defense.

The work involves the isolation, synthesis and characterization of the natural products, interaction studies with cells, artificial membranes and membrane proteins by a variety of spectroscopic methods. The ultimate goal is to establish a structure-function relationship of insecticidal action, and to identify possible synergistic relations between the components.

Candidates are required to have obtained a very good MSc in Biochemistry, Biophysics, Molecular Biology, Chemistry or closely related field and should be fluent in English. Previous experience in molecular biology, cell culture, lipid biophysics and/or spectroscopy are a strong plus. For the PhD student isolating and/or synthesizing the peptides (Bode laboratory) a strong expertise in organic synthesis (solid phase peptide or even natural product synthesis), mass spectrometry (HPLC-ESI-MS) is required.

Two of the successful applicants will carry out their work at Mainz University, Institute for Biochemistry and will collaborate closely with the working group of Helge Bode, Molecular Biotechnology, Goethe University Frankfurt, where the third PhD-student will be located (please specify in your application which lab you want to join.

Where
The group of Helge Bode, Merck-Professorship for Molecular Biotechnology, Biosciences & Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Biocenter Campus Riedberg (N250, EG), Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, h.bode@bio.uni-frankfurt.de, +49 69 798 29557.

Project specific requirements
Keywords: Chemical synthesis (solid phase peptide synthesis), natural product isolation, HPLC-MS analysis, chromatography, structure elucidation of natural products (MS and NMR).

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Where
The group of Nadja Hellmann, Institute for Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany, Email: nhellmann@uni-mainz.de, phone: +49 (0)6131 392 5836 .

Project specific requirements
Keywords: Biophysics, thermodynamics, optical spectroscopy, artificial membranes

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Where
The group of Ute Hellmich, Department of Pharmacy and Biochemistry, Membrane Biochemistry, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany, Email: u.hellmich@uni-mainz.de, phone: +49 (0)6131 39 26182.

Project specific requirements
Biophysics, NMR spectroscopy, (protein) structure/function relationship, membrane transporters, protein-substrate/protein-lipid interactions.

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Project 4: Targeted manipulation of membrane dynamics by synthetic molecules.

Project description
Mitochondria are double-membrane enclosed eukaryotic organelles with a number of essential functions. Best known is the generation of adenosine triphosphate (ATP) via oxidative phosphorylation at the inner membrane. Impairments in mitochondrial function lead to degeneration of biological systems, disease (e.g. neuromuscular diseases, Parkinson's disease) and aging. We use the filamentous fungus Podospora anserina as a model for the elucidation of components and mechanisms involved in the control of organismic aging Previous work demonstrated a key role of mitochondria in this process. In particular, we demonstrated an impact of processes at the inner mitochondrial membrane, at which most of the cellular ATP is generated and, as by-products, also reactive oxygen species (ROS). At low levels, these reactive molecules are essential for correct development. In contrast, increased ROS levels lead to damage of all kinds of cellular molecules including nucleic acids, proteins and lipids. As consequence mitochondrial function declines.

In the new project we will focus on the impact of the phospholipid cardiolipin, which is enriched in the inner mitochondrial membrane. Cardiolipin is known to affect the activity of membrane proteins, membrane structure and dynamics. In the project we will specifically address the question whether molecules that interact with cardiolipin can be effective in stabilizing the inner mitochondrial membrane leading to improved mitochondrial functions (e.g., respiration) and an increase in healthy lifespan. We will employ established (e.g., respiration measurements, genetic manipulation by transformation, microscopy) and new techniques. The expected results will be of special interest for translation from P. anserina to other species and in particular for the elucidation of the mechanisms of aging and interventions into this process of humans.

Where
The group of Heinz D. Osiewacz, Molecular Biosciences, Molecular Developmental Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, N 200-206, 60438 Frankfurt am Main, Germany, Email: Osiewacz@bio.uni-frankfurt.de, +49 (0)69  798 29264.

Project specific requirement
Strong background in molecular biology, cell biology, and biochemistry. Experience in handling of fungi will be very helpful.
Keywords: Aging, healthy lifespan, mitochondria, cardiolipin, fungi.

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Project 5: Targeted modulation of membrane dynamics via small molecules.

Project description

Mitochondria are critically involved in many cellular processes, such as aging and apoptosis. In fact, dysfunction of mitochondria results in accelerated aging and can lead to severe diseases. Changes in the ultra-structure and dynamics of mitochondrial membranes are involved in aging processes, and the mitochondrial inner membrane appears to be especially vulnerable, due to the generation of reactive oxygen species in the respiratory electron transfer chain.

We aim to control mitochondrial processes via modulating the structure and dynamics of mitochondrial membranes. In our project, we will specifically target the mitochondrial inner membrane by small molecules that interact explicitly with this membrane system.

The membrane lipid cardiolopin, a lipid of bacterial origin, is present almost exclusively in the mitochondrial inner membrane, and thus it is a “marker-lipid" for this organelle. Consequently, our goal is to identify small molecules that interact specifically with cardiolipin, thereby modulating the dynamics and function of the mitochondrial inner membrane.

In our project, we work together with the group of T. Bereau (Max-Planck-Institute of Polymer Research Mainz) who identifies potential candidate structures using a computational approach. The cardiolipin binding specificity, the membrane modulation capacity and the overall impact on a membrane structure and activity will be tested and analyzed in our group. “Hot" candidates will then tested in the fungi Podospora anserina, an established model for studies on mitochondrial membrane dynamics and alterations associated with aging and certain diseases.

Our identification of cardiolipin interactors will not only help us to better describe and understand the dynamics of mitochondrial membranes, but will also enable us to directly target and modulate processes that involve mitochondria, such as aging and apoptosis.

Where
The group of Dirk Schneider, Institute for Pharmacy and Biochemistry, Membrane Proteins , Johannes Gutenberg-University Mainz,
Johann-Joachim-Becher-Weg 30, 55128 Mainz, Germany, Email: Dirk.Schneider@uni-mainz.de, +49 (0)6131 39 25833 .

Project specific requirements
We are looking for motivated and talented PhD student with a background in biology, (bio)chemistry or biophysics. We expect that you have a strong interest in chemical-biology and membrane biochemistry/biophysics. Ideally, you have experience in molecular, biochemical and biophysical techniques, which is apparent from your CV. We are looking forward to your application! International applicants are very welcome.  Keywords: membrane biology, biochemistry, biophysics, chemical-biology.

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Project 6: Membrane dynamics by vectorial lipid organization.

Project description
Lipid flux and transfer are hot and emerging topics in advanced cell biology, biochemistry, and biophysics, intimately linked to human health and diseases. Our project aims to study the asymmetric lipid organization and its influence on membrane deformation and the lateral organization of membrane proteins and signaling modules. We have recently identified specific lipid flippases, which allow us to control the vectorial lipid flux between different lipid leaflets in an unprecedented manner, controlling membrane dynamics, curvature and shape.

Where
The group of Robert Tampé, Institute for Biochemistry, Cellular Biochemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, Email: tampe@em.uni-frankfurt.de, +49(0)69 798 29475.

Project specific requirements
Science is fun! If you are inspired and hooked on by transdisciplinary research, applying cutting-edge techniques in protein biochemistry, biophysics, microscopy, molecular and structural biology, please apply. Our international team consists of motivated biochemists, molecular and cell biologists, chemists, and biophysicists.

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Project 7: Tailor-made synthetic molecules for directed membrane perturbation.

Project description
Lipids are ubiquitous and dynamic regulatory molecules and their biological functions depend on their subcellular locations as well as local concentrations. The project aims to develop and design novel chelator lipids and lipid surrogates that can be activated and/or redistributed upon external stimuli. In addition, the side-directed functionalization of lipids for their on-demand reallocation is aspired. The project includes the synthesis of stimuli-responsive lipids and lipid-anchored chelators, their biophysical characterization as well as in vitro studies in model membranes. Ultimately, in vivo analysis of the developed compounds is intended.

Where
The group of Ralph Wieneke, Cellular Biochemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany, wieneke@em.uni-frankfurt.de, +49 (0)69 798 29477.

Project specific requirements
Strong background in chemistry, biochemistry or chemical biology, experience in (membrane) biochemistry and fluorescence microscopy will be very helpful, interest in the development of synthetic molecules to elucidate molecular mechanisms in membrane biochemistry. Keywords: Organic synthesis, membrane protein biochemistry, fluorescence microscopy, artificial membranes.

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Projects in Cellular Modelling of membrance dynamics

Project 8: Membrane dynamics and its role in pathogenesis of multiple myeloma.

Project description
Multiple myeloma is often accompanied by severe osteolytic bone lesions leading to bone destruction and secondary osteoporosis. The bone disease has a major influence on patient morbidity, and is significantly shaped by the interaction of malignant plasma cells with osteoclasts. Osteoclast function depends on the endolysosomal system, through which vesicular transport of membrane components to/from the plasma membrane is facilitated. Rab-GTPases play an important role in controlling these transport processes, especially Rab7, which is e.g. involved in recycling of mannose-6-phosphate receptor, in fusion of autophagosomes with lysosomes  and in EGF receptor degradation. However, until now, the molecular mechanisms triggering loss of osteoclast function in myeloma patients are unclear. We postulate that the interaction of  Rab7 with adaptor protein Plekhm1  and HOPS complex proteins is relevant in this context. The project therefore aims at analyzing the role of Plekhm1 in Rab7/HOPS-mediated membrane dynamics , especially with respect to perinuclear endosomal attachment und endolysosomal fusion. It is carried out in collaboration with the groups of Prof. Hubert Serve and Dr. Ivana von Metzler, who will evaluate the role of the Rab7-Plekhm1-HOPS interaction in multiple myeloma pathogenesis. Following the analysis of critical factors in membrane dynamic and their molecular interactions, we strive to identify peptides to manipulate these processes.

Where
The group of Ivan Dikic, Institute of Biochemistry II, University Hospital Frankfurt, Johann Wolfgang Goethe-University Frankfurt, Theodor-Stern-Kai 7 / Building 75, 60590 Frankfurt am Main, Germany, Email: Dikic@biochem2.uni-frankfurt.de, +49 (0)69 6301 5964.

Project specific requirements

Strong background in biochemistry, cell and/or molecular biology, experience in  cell culture (e.g. with co-culture models), proteomic analysis and/or advanced microscopy will be very helpful. Keywords: endolysosomal transport, manipulation of membrane dynamics, Plekhm1, Rab GTPases, multiple myeloma bone disease. 

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Project 9: Characterization of FGF-induced FGFR-receptor oligomerization by NMR and advanced light microscopy.

Project description

Where
The group of Harald Schwalbe, Institute for Organical Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, N160-3.13, 60438 Frankfurt am Main, email: schwalbe@nmr.uni-frankfurt.de , +49 (0)69 798 29737.

Project specific requirements
Study of Biochemistry or Chemistry, Master in either of the two topics. Interests in biochemical preparation of molecules and spectroscopic characterization. Keywords: Biochemical preparation, NMR spectroscopy, maintaining collaborative research with DynaMem.

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Project 10: Manipulation of mitochondrial properties by altering the mitochondrial fatty acid synthase (FAS).

Project description
The project aims at elucidating the influence of the chain length of fatty acids on the fatty acid/lipid metabolism in mitochondria. In a manipulative approach, the mitochondrial FAS is changed in chain length control so that fatty acids with different chain length can be produced. Methods comprise the in vitro characterization of proteins and their product spectra, the analysis of isolated mitochondria, and the evaluation of changed morphological and physiological properties of mitochondria within complete cells.

Where
The group of Martin Grininger, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Strasse 5, 2.630, 60438  Frankfurt am Main, Germany, Email: Grininger@chemie.uni-frankfurt.de, +49 (0)69 798 42705.

Project specific requirements
The successful candidate has a profound knowledge about proteins in their structural and functional properties, and is interested in elucidating molecular mechanisms of biological processes. Lab experience by working on chemical/biological projects is obligatory for a successful application.
Keywords: protein engineering, structural biology, molecular mechanism, lipid metabolism.

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Projects in Dynamics of membrane systems and organelles

Project 11: Dynamics of organelles and organelle surrounding membranes.

Project description
The dynamics of organelles, the stress-induced transport of galactolipids synthesized in plastid, the lipid composition of membranes and the composition of the membrane inserted and associated proteins are central for maintenance of cellular functions. Trigger for dynamic changes of the structure of membranes are changes of protein-to-lipid-ratios during development, changes of the nutrition in the environments e.g. of phosphate or other environmental parameters like the temperature. One observed form of adaptation is the formation of membrane excrescences. For example, the formation of plastidic stromules is discussed as one form of the enlargement of membrane surfaces. However, stromules are formed under normal conditions as well and are discussed to serve as platform for the interaction between plastids and other organelles for signal transduction. Although stromules have been discovered as early as in the sixties of the last century, the molecular mechanism of their formation and dynamics is still under investigation. Beside formation of membrane extrusions, positioning of organelles within cells is a second constrain for cellular function. The light-induced repositioning of chloroplasts is a prime example for this dynamics. Again, while for some specific processes a detailed picture is emerging, the general mechanisms of organelle mobility and deformation. The aim of the project is the description of the dynamics of mitochondria and plastids and its relation to the lipid composition and protein association and integration. The project will be conducted in collaboration with the groups of E. Stelzer (Frankfurt), a leading expert in the field of high resolution microscopy and F. Schmid (Mainz), a leading expert in the formulation of mathematical-physical Models for the description of membranes.

Where
The group of Enrico Schleiff, Institute for Molecular Biosciences, Plant Cell Physiology, Johann Wolfgang Goethe-University Frankfurt, Biozentrum, Campus Riedberg, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Email: schleiff at bio.uni-frankfurt.de, +49 (0)69 798 29287.

Project specific Requirements
The applicant should have completed the studies in the subject biology, biochemistry, cell biology or biophysics. The applicant should have experience in either plant cell biology or light and fluorescence microscopy. The applicant should be highly motivated to work in an interdisciplinary project in plant biology. Keywords: organic synthesis, membrane protein biochemistry, fluorescence microscopy, artificial membranes

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Project 12: Quantitative Dynamic Light Sheet Fluorescence Microscopy.

Project description
Novel contrasts and optical arrangements will be developed that support the observation of multicellular biological objects. The instrument will be applied in experiments in plants, mammalian cells and small model organisms. An essential goal is to gather three-dimensional data sets, which provide excellent quantitative information. The data will be evaluated in collaboration with consortium partners.

Where
The group of Ernst Stelzer, Institute of Cell Biology & Neuroscience, Buchmann Institute for Molecular Life Sciences (BMLS, CEF-MC), Physical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany, Email: ernst.stelzer@physikalischebiologie.de, stelzer@bio.uni-frankfurt.de, +49 (0)69 798 42547.

Project specific Requirements
Keywords: SPIM, DSLM, LSFM, multi scalar, fluorescence.

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Project 13: Data analysis and modeling for spatio-temporal dynamics of cell-cell interactions.

Project description
The group of F. Matthäus focuses on the development of data analysis approaches and mathematical models for cell motility with regard to intracellular regulation, mechanical and chemical cell-cell interaction, and collective phenomena in large cell populations.

In DynaMem, project P9, we are involved in the data and image analysis for 3D time lapse fluorescence microscopy as well as 3D electron microscopy. Applications involve the dynamics of cell-cell interactions in 3D multicellular systems, such as cancer spheroids and insect embryos. Hereby, our aim is the application and development of analysis approaches (segmentation, tracking, particle image velocimetry) to derive spatio-temporally resolved quantitative information (structure, motion, density) from the data. This information will then provide the base for the development of mathematical models describing the evolution of the cell systems. The models are usually given in terms of systems of ordinary, stochastic or partial differential equations, as well as hybrid models, where discrete agents are coupled with continuous variables describing the environment. .

Where
The group of Franziska Matthäus, Johann Wolfgang Goethe-University Frankfurt, Frankfurt Institute for Advanced Studies (FIAS), Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany, Email: matthaeus@fias.uni-frankfurt.de, +49 (0)69 798 47509.

Project specific Requirements
We are looking for students holding a masters degree in physics, mathematics, computer science, or theoretically oriented life sciences. Very good programming and communication skills, interest in biological systems and in interdisciplinary collaboration are expected. In this project we deal with large data sizes (several TB for raw image data is common). Experience with parallel programming and code implementation for graphic cards is highly welcome. Keywords: Very good programming & communication skills, solid mathematical background, experience in data science or image analysis.

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