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Open Doctoral Positions 2019

Doctoral projects offered by LSM faculty members for 2019 (last updated: 16.10.2019)

Should you have any questions regarding the announced projects, please do not hesitate to contact the project supervisor !

Supervision: Prof. Dr. Dario Leister (Plant Molecular Biology/Botany)

Title: Acclimation in photosynthesis

Photosynthesis is a complex process that is also highly dynamic in response to changes in environmental conditions. We study this flexibility at multiple levels including communication between the chloroplast and the nucleus to reprogram nuclear gene expression, as well as at the level of thylakoid membrane complexes by switching between linear and cyclic electron flow. We apply a battery of techniques, ranging from genetic screens, molecular biology, biochemistry and biophysics to quantitative biology approaches.

Supervision: Prof. Dr. Stylianos Michalakis (Epigenetics, Bioinformatics)

Title: Role of TET-mediated 5mC oxidation for neuronal differentiation and plasticity

Scientific background: Neuronal networks show a remarkable degree of plasticity during physiological and pathophysiological processes. This plasticity goes along with major adjustments in the expression of key genes. The mechanisms controlling gene expression and neuronal plasticity are not well understood, but it is suggested that epigenetic mechanisms such as DNA methylation contribute crucially to these biological processes. Methylation of the DNA base cytosine is catalyzed by DNA methyltransferases (DNMT) and occurs at the C-5 position of the cytosine base resulting in 5-methylcytosine (5mC). Removal of the methyl group involves oxidation by TET methylcytosine dioxygenases. The overarching goal of this project is to help improving our understanding on how TET enzymes and 5mC oxidation products shape the epigenome of neurons and influence CNS function.

Specific aims and methodology: The functional significance of TET proteins and their enzymatic products in the CNS has not been characterized and will be addressed in this project with specific genetic mouse and cellular models. TET enzymes act in concert with chromatin remodeling proteins and transcription factors. We identified intriguing novel TET interaction partners in mouse retina, mouse brain and/or induced pluripotent stem cell (iPSC)-derived neurons. The potential of these proteins to engage with the TET3 isoform and modulate its enzymatic activity will be assessed in this proposal. We are looking for a highly motivated PhD candidate with bioinformatic, genetic and epigenetic background and strong interest in neuroscience. The candidate will apply bioinformatic methods and will also have the chance to learn and apply genetic, biochemical, cell biological and viral gene transfer methods in vitro and in vivo.

Further information and selected literature:

M. Wagner, J. Steinbacher, T. F. Kraus, S. Michalakis, B. Hackner, T. Pfaffeneder, A. Perera, M. Müller, A. Giese, H. A. Kretzschmar, T. Carell, Angew Chem Int Ed 2015, 54, 12511-12514.
A. Perera, D. Eisen, M. Wagner, S. K. Laube, A. F. Künzel, S. Koch, J. Steinbacher, E. Schulze, V. Splith, N. Mittermeier, M. Müller, M. Biel, T. Carell, S. Michalakis, Cell Rep 2015, 11, 283-294.

T. Pfaffeneder, F. Spada, M. Wagner, C. Brandmayr, S. K. Laube, D. Eisen, M. Truss, J. Steinbacher, B. Hackner, O. Kotljarova, D. Schuermann, S. Michalakis, O. Kosmatchev, S. Schiesser, B. Steigenberger, N. Raddaoui, G. Kashiwazaki, U. Müller, C. G. Spruijt, M. Vermeulen, H. Leonhardt, P. Schar, M. Müller, T. Carell, Nat Chem Biol 2014, 10, 574-581

Supervision: Prof. Dr. Thomas Nägele (Plant Evolutionary Biology)

Title: Quantitative Simulation of Subcellular Plant Metabolism

Funding for this project "Quantitative Simulation of Subcellular Plant Metabolism" is still pending, therefore the applicant might need to have his/her own funding (Scholarship,stipend,...)

Background and Motivation

Environmental fluctuations frequently result in abiotic stress conditions for plants which have a major impact on their yield and productivity. Temperature is among the most important abiotic factors that shape the geographic range of many plant species and strongly influence agricultural productivity in temperate regions. For the genetic model plant Arabidopsis thaliana, range boundaries are defined by low winter temperatures in northern and eastern Eurasia, and it was demonstrated that cold and freezing tolerance of local populations of Arabidopsis correlates with habitat winter temperatures from Scandinavia down to the Iberian Peninsula. The availability of diverse natural accessions with distinct cold acclimation capacities has made Arabidopsis an important model system to study underlying molecular mechanisms. Combining data on natural genetic variation of Arabidopsis thaliana with enzyme kinetics, metabolite concentrations and physiological parameters is the next crucial step to study genotype-phenotype relationships. This needs mathematical in silico models to provide quantitative insight into metabolic regulation which is essential for our understanding of plant stress response, its ecological significance and evolutionary conservation.

Aim of the project

The aim of this project is to develop and apply a quantitative kinetic model of subcellular plant metabolism to unravel central conserved strategies of metabolic reprogramming and natural stress tolerance in the genetic model plant Arabidopsis thaliana. Currently, the lack of such a quantitative model strongly limits our understanding of plant growth, development, ecology and evolution. The impact of environmental changes on plant energy conversion and carbohydrate metabolism is only vaguely understood because of a tightly regulated and highly complex molecular network which enables plants to survive under unfavourable environmental conditions. In previous work, we have developed a setup of experimental techniques and mathematical methods which enables us to quantify kinetics of subcellular metabolism. A combination of mathematical modelling, subcellular metabolomics and enzyme kinetic analyses will be applied to explain natural variation of Arabidopsis thaliana stress response in context of plant physiology, ecology and evolution.

Further Information

Fürtauer, L., Küstner, L., Weckwerth, W., Heyer, A.G. and Nägele, T. (2019) Resolving subcellular plant metabolism. Plant J, https://doi.org/10.1111/tpj.14472

Weiszmann, J., Fürtauer, L., Weckwerth, W. and Nägele, T. (2018) Vacuolar sucrose cleavage prevents limitation of cytosolic carbohydrate metabolism and stabilizes photosynthesis under abiotic stress. FEBS J, 285, 4082-4098, https://doi.org/10.1111/febs.14656

The 1001 Genomes Consortium (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell, 166, 481-491. https://doi.org/10.1016/j.cell.2016.05.063

Supervision: Dr. Tamara Mikeladze-Dvali (Cell and Developmental Biology)

Title: Molecular Mechanisms regulating centrosome assembly and stability

With this project "Molecular Mechanisms regulating centrosome assembly and stability" the applicant is not guaranteed a funded position, however he/she need to have their own funding (Scholarship,stipend,...)

Centrosomes are the major microtubule organizing centers of animal cells. Centrosome components have diverse functions in many different cell biological processes, ranging from cell division to cell polarity and signaling. Deregulation of centrosomal components can lead to human conditions as cancer and microcephaly. Therefore, our research is focused on deciphering molecular mechanisms regulating centrosome dynamics in a living organism. In the recent years the centrosome has emerged a highly structured and dynamic organelle. It comprises a pair of centrioles surrounded by layers of pericentriolar material (PCM). In nonmitotic cells the PCM forms a thin layer (core) around the centrioles. When cells enter mitosis the PCM dramatically expands into a spherical mitotic centrosome, facilitating microtubule nucleation. SPD-5 (the functional homologue of the human microcephaly-linked protein, CDK5RAP2), SPD-2 (human Cep192) and the Polo-like-kinase-1, PLK-1 are part of an evolutionary conserved module driving mitotic PCM dynamics. In C. elegans SPD-5 is the main PCM matrix protein. It forms the non-mitotic PCM core and expands during mitosis in a SPD-2 and PLK-1-dependnet manner, providing the basis for robust microtubule nucleation and the formation of a bipolar spindle. Recently we identified a novel centrosomal protein PCMD-1 and demonstrated that PCMD-1 regulates dynamics of the SPD-5/SPD-2/PLK-1-module at the centrosome. In particular, in absence of PCMD-1 function targeting of SPD-5 to the non-mitotic centrosome core is abolished. As a result the integrity of the SPD-5-containing centrosome matrix at mitosis is severely compromised and the formation of a bipolar spindle is disrupted. However, how exactly PCMD-1 regulates centrosome matrix stability and robustness remains an open question. We offer a PhD project, which builds on our current knowledge of PCMD-1 function. The aim is to dissect details of PCMD-1 interaction with centrosomal matrix proteins and cell cycle regulators. The proposed project will use a variety of state of the art microscopy approaches, genetic and biochemical techniques in the nematode C. elegans.

Selected references:
1. Erpf AC., Stenzel L., & Mikeladze-Dvali T. PCMD-1 organizes centrosome matrix assembly
in C. elegans. Current Biology 29, 1324–1336 (2019).

2. Woodruff JB., Wueseke O., & Hyman AA. Regulated assembly of a supramolecular
centrosome scaffold in vitro. Science 348, 808–812 (2015).

3. Woodruff JB., Ferreira Gomes B., & Hyman AA. The centrosome is a selective condensate
that nucleates microtubules by concentrating tubulin. Cell 169, 1066–1077 (2017).
Approval for funding is pending

Supervision: Prof. Dr. Christof Osman (Cell and Developmental Biology)

Mitochondria are known as the power plants of our cells, because they produce a large amount of ATP through oxidative phosphorylation (OXPHOS) and supply our cells with energy. Several crucial proteins required for OXPHOS are encoded on the mitochondrial genome (mtDNA). Cells must therefore ensure maintenance of functional mtDNA to secure their efficient energy supply and health. Accordingly, mutations in mtDNA can have dire consequences and can lead to mitochondrial diseases and ageing. Quite surprisingly, fundamental questions regarding the biology of mtDNA are currently poorly understood: How is mtDNA faithfully passed on to daughter cells? How are mtDNA copies distributed throughout the mitochondrial network? How is the integrity of mtDNA maintained over generations? It is these mysteries that fascinate us and that we aim to unravel, down to a deep mechanistic understanding. The answers to these question also hold the key for a better understanding of human mitochondrial disorders and will pave the way for the development of new therapeutical approaches. To study mitochondria and mtDNA, we combine unique experimental advantages in the model organism S. cerevisiae with a wide variety of cell biological techniques, including fluorescent live-cell and super-resolution microscopy, next-generation sequencing, protein biochemistry and yeast genetics.

Two projects are are available in our lab:

Project 1: Elucidation of the molecular mechanisms that determine the spatio-temporal dynamics and organisation of mtDNA within the mitochondrial network

This project will have a strong focus on different microscopy-techniques (including super-resolution microscopy) and image analysis (Fiji, Python, R)

Project 2: Identification of the molecular machinery that detects and removes mutated mtDNA from mitochondria.

This project will involve a wide spectrum of cell biological methods and yeast genetics.

For more information on publication please click here.

Supervision: Prof Dr Martin Parniske (Genetics, Plant biology )

Project 1; Title: Molecular inventions underlying the evolution of the nitrogen-fixing root nodule symbiosis.

Crop production worldwide is sustained through nitrogen fertilizer produced via the energy-demanding Haber-Bosch process. One group of closely related plants evolved to become independent of nitrogen from the soil by engaging in symbiosis with bacteria that convert atmospheric nitrogen to plant-usable ammonium and are hosted within specialized organs, the root nodules. Nodulation evolved several times independently but exclusively in four related orders, the Fabales, Fagales, Cucurbitales and Rosales (FaFaCuRo) based on a putative genetic predisposition to evolve root nodules acquired by a common ancestor of this clade.
The doctoral project will contribute to a larger ongoing effort of the Parniske lab to identify the elusive genetic switches involved in the evolution of nodulation. It builds on the underlying idea that a succession of events co-opted preexisting developmental programs to be activated by symbiotic stimuli. We will systematically investigate and compare the prewired connections between signaling pathways and developmental modules present in non-nodulating and nodulating relatives, to identify components acquired by nodulators. The Rosaceae represent a particularly attractive family to test evolutionary hypotheses by transferring candidate switches from a nodulator into the genome of closely related sister genera to enable nitrogen fixing root nodule symbiosis. Most genera of the Rosaceae including economically valuable targets such as apple and strawberry are non-nodulating. A minority of Rosaceae form ancestral, lateral root related actinorhiza nodules with Frankia actinobacteria, which differs from the derived, more complex symbiosis of legumes with rhizobia. Frankia strains have a very broad host range and can fix nitrogen at ambient oxygen concentrations thus imposing minimal constraints on a host environment suitable for efficient symbiosis. Thus, by retracing small evolutionary steps within the Rosaceae we will take a huge leap towards nitrogen-fertilizer independent crops for sustainable agriculture.

Project 2; Title:Sequence adaptations in the symbiosis receptor-like kinase (SymRK) enabeling nitrogen-fixing root nodule development

Plant root symbioses with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing bacteria bear huge potential for sustainable agriculture by reducing the chemical fertilizer input required to maintain high crop yields. The regulation and signal transduction mechanism leading to AM and the nitrogen-fixing root nodule symbiosis (RNS) share a genetic toolkit largely conserved across land plants. It contains a set of signal transduction components including the Symbiosis Receptor-like Kinase SymRK. During evolution, SymRK appears to have acquired novel molecular features that facilitated the development of the nitrogen-fixing root nodule symbiosis, while maintaining its conserved function for AM. In this project, we will explore sequence diversity among SymRK orthologs and paralogs with the goal to narrow down and identify critical sequence adaptations that underlie the rhizobial infection of plant cells. The doctoral student will investigate the mechanistic consequences of these adaptations at the cell biological and biochemical level with a focus on interacting proteins. The relevance of SYMRK paralogs and interacting proteins will be explored by reverse genetics utilizing transposon insertion populations or CRISPR/CAS genome editing technology and quantitative binding studies in vivo using advanced light microscopy and in vitro using a range of state-of-the-art technologies. We expect novel insights into the molecular mechanisms facilitating the symbiotic infection process of plant cells by nitrogen fixing bacteria.

Project 3; Title: Spatio-temporal dynamics in the composition and function of the CCaMK/CYCLOPS complex

Plant root symbioses with arbuscular mycorrhiza (AM) fungi and nitrogen-fixing bacteria bear huge potential for sustainable agriculture by reducing the chemical fertilizer input required to maintain high crop yields. The regulation and signal transduction mechanism leading to AM and the nitrogen-fixing root nodule symbiosis (RNS) share common components including the calcium and calmodulin dependent protein kinase (CCaMK) and its phosphorylation target CYCLOPS, a DNA binding transcriptional activator (Tirichine et al., 2006; Yano et al., 2008; Singh et al., 2014). The CCaMK/CYCLOPS complex is a central regulatory hub in symbiosis signaling. It controls the expression of three transcriptional regulators of three distinct developmental programs. NIN controls nodule organogenesis and, together with ERN1, infection thread formation while RAM1 is indispensable for arbuscule development (Singh et al., 2014; Pimprikar et al., 2016; Cerri et al., 2017). The corresponding promoters control distinct timing, expression domains and response to different stimuli. The promoter choice and activity of CCaMK/CYCLOPS must therefore be coordinated at a spatio-temporal and a stimulus-specific level to trigger appropriate cell developmental programs. In the past, we identified additional putative complex components that may contribute to binding of diverse cis regulatory elements within the known target promoters of CCaMK/CYCLOPS. The doctoral student will study the relevance of the identified additional complex components using a range of techniques, including reverse genetics utilizing transposon insertion populations or CRISPR/CAS genome editing technology. The spatio-temporal composition of the complex and its structural rearrangement will be studied via in vivo FRET-FLIM in root hair nuclei in response to signals emanating from arbuscular mycorrhiza fungi or nitrogen-fixing bacteria. Biochemical in vitro measurements will be used to quantify protein-protein and protein-DNA binding affinities. We expect to unravel key steps in the molecular dynamics of the CCaMK/CYCLOPS complex underlying the specific activation of the appropriate and distinct developmental programs in response to fungi and bacteria and thus the establishment of AM and root nodule symbioses.

toSupervision: Dr. Silke Robatzek (Genetics)

Title: Identification of the molecular basis of plant susceptibility mediated by microbe-derived extracellular vesicles. 4-year doctoral project, description:

The project is funded by the DFG Collaborative Research Centre 924 Molecular mechanisms regulating yield and yield stability in plants (Yield) and will identify the molecular basis of plant susceptibility mediated by microbe-derived extracellular vesicles. Reducing crop losses from disease epidemics caused by pathogens is critical to stabilize yields.
Infection success of pathogens depends on the delivery of virulence factors into host cells to suppress host immunity. Extracellular vesicles (EVs) represent structures important in bacterial-host communication and have the capacity to modulate the plant’s immune response. How bacterial EVs modulate the plant immune system and how immune modulation leads to infection control is currently not understood. We will address these questions using state-of-the-art proteomics methods combined with cell biology and genetic mutants, and aim to transfer our findings into relevant crops. At its completion, this project will lead to new insights into mechanisms controlling plant resistance. This will pave the way for an improved understanding of a fundamental question in plant-pathogen interactions.

 

Supervision: Dr. Irina Solovei (Human Biology and Bioimaging )

Title: Spatial Arrangement of Expressed Genes in the Nucleus.

Knowledge pertaining to the fine molecular mechanisms of transcriptional activation and regulation, including co- and post-transcriptional processes, is rapidly expanding. Similarly, the transcriptional importance of global genomic arrangement, illustrated by the spatial segregation of transcriptionally active euchromatin from inactive heterochromatin, is widely appreciated and studied. However, our knowledge regarding an intermediate level of transcriptional organization, relating to the spatial arrangement of individual transcribed genes, is surprisingly limited.

One of our project is focused on studying of genes, which are both long (>100 Kb) and highly expressed. These two features make transcribed genes microscopically resolvable and allow study their spatial arrangement in the context of the cell nucleus. The preliminary data obtained so far show that expressed genes loop out of harboring chromosomal locus and form so called transcription loops, with RNA polymerases moving along gene axes and carrying nascent RNA transcripts. Our current hypothesis is that transcription loop formation is one of the universal principles of eukaryotic gene expression, which has not been appreciated until now due to the resolution limits of light microscopy and due to the low expression of studied genes.

Our methods include standard cell biology experimental work, molecular biology (such as RNAseq, ChIPseq, 3C-techniques), gene engineering (CRISPR/Cas9), fluorescence in situ hybridization (2D- and 3D-FISH), all types of light microscopy (wide field, confocal and high resolution microscopy), histology (mostly cryosections), electron microscopy, etc.

Supervision: Dr. Arne Weiberg, Prof. Martin Parniske (Genetics, Plant biology)

Title: Small RNA warfare in plant-pathogen interactions

Plant pathogens send small RNA effectors into plants to manipulate host physiology and immune response, a mechanism called cross-kingdom RNAi. Our lab is interested in understanding the molecular principles of RNA transport from pathogens into plant cells.
In this project, we aim at discovering the means of RNA transport by a combination of complementary biochemical, genetics and bioinformatics approaches. In particular, we propose that RNA-binding proteins (RBPs) that form ribonucleoprotein complexes (RNPs) play a pivotal role in RNA sorting for secretion and transport. Moreover, we identified extracellular vesicles produced by plant pathogens that might deliver RNAs from pathogens to plants. Our lab has established standard methods of RNA-protein interaction studies, such as co-immunopurification of RBPs (e.g. Argonaute-small RNA complexes) coupled to next-gen sequencing. In this project, established as well as novel methods to investigate RBPs should be applied to unravel the role of candidate RNPs and extracellular vesicles in cross-kingdom RNAi.

Supervision: Dr. Esther Zanin (Cell and Developmental Biology)

Title: Molecular mechanisms controlling cell division

Our group is interested in the molecular mechanisms that control cell division. During the last step of cell division, a process called cytokinesis, the mother cell splits into two daughter cells. When the chromosomes segregate in anaphase a contractile actin-myosin ring assembles underneath the plasma membrane. Contractile ring formation has to be spatially and temporally coordinated with chromosome segregation to ensure that the genomic content is properly distributed. Cytokinesis failure results in tetraploidy and supernumerary centrosomes causing multipolar spindles and oncogenic transformations. The aim of the PhD project is to delineate the molecular pathways that control cytokinesis in time and space. In our research group we combine the advantages of both the nematode C. elegans and tissue culture cells. As our main approach we use quantitative live-cell microscopy since it provides the high temporal and spatial resolution required to study such a dynamic process like cytokinesis. In addition to live-cell microscopy we apply a broad range of cell biological techniques including biochemistry, molecular biology, genetics and screening approaches. Our research group is part of the cell- and developmental biology department, which not only offers high-end instrumentation and laboratory equipment but also a highly interactive and international research environment. We are searching for highly motivated applicants with a strong interest in fundamental questions of cell biology. Applicants should have excellent knowledge of cell and molecular biology and hold a master degree in life science.
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