PhD Projects 2014

PhD projects offered by LSM faculty members to applicants for 2014:

Please note:

• You have to apply with our online application tool.
• If the available PhD projects don’t match your interest you are free to add to your online application tool a proposal for the research you would like to perform in a research group belonging to the LSM-faculty (http://www.lsm.bio.lmu.de/faculty/).
• Please click on the name of the supervisor to get redirected automatically to further information on the research group and the scientific contents. 

Supervisor: Prof. Martin BIEL (Pharmacology, Genetics, Molecular Biology)

Title: Regulation of two pore channels (TPCs) in central nervous system

Two-pore cation channels (TPC1 and TPC2) are members of the TRP channel superfamily. A characteristic feature of TPCs is their intracellular localization in the endolysosomal system. TPCs are broadly expressed in the body and have been supposed to be involved in multiple cellular processes including Ca2+ signaling and control of endolysosomal trafficking. In this project we will make use of TPC1- and TPC2-deficient mouse lines to dissect the physiological role of TPCs in the central nervous system. The project will employ a variety of methods including cell biology methods, electrophysiology, Ca2+ imaging, FRET and confocal microscopy.

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Supervisor: PD Dr. Bettina BOELTER /Prof. Juergen SOLL (Plant Sciences, Biochemistry, Molecular Biology)

Title 1: Overcoming barriers - protein import into chloroplasts

Protein import into chloroplasts is an essential process, which relies on complex translocation machineries. Our focus is the translocon at the inner envelope membrane, TIC. The current project deals with an yet quite enigmatic Tic component, which is evolutionary highly conserved and seems therefore indispensible for photosynthetic organisms. We are searching for interaction partners and are investigating its role in the import process.

Title 2: Characterization of channel proteins

A second project deals with the functional characterization of protein conducting channel proteins in the TIC complex. We have identified two Tic components, which form a channel in vitro and have distinct properties. We want to further analyze channel characteristics and regulative features especially by electrophysiology and therefore look for a candidate with experience in this method.

Further information: http://www.en.botanik.bio.lmu.de/research/soll/subgroups/b__lter/index.html

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Supervisor: Prof. Michael BOSHART (Genetics, Biochemistry, Cell Biology)

*Title: Temperature control of parasite life cycle development – a cold responsive signaling pathway in Trypanosoma

Low temperature co-triggers development of protozoan parasites like Trypanosoma and Leishmania when they shuttle between mammalian and arthropod hosts. We identified a protein kinasse in T. brucei that is activated by cold temperature and the PhD project contributes to genetic dissection of the cold signaling pathway. The key problem is the identity of the thermosensor and the signaling upstream of the protein kinase. Exploiting the distant position of protozan parasites in the tree of life, we expect insight into the evolution of fundamental mechanisms of cell signaling. Our model organism is closely related to important tropical pathogens, causing severe and difficult to treat human diseases. Exotic molecular mechanisms are attractive targets for drug development. Methods include genome wide RNAi screening and protein-protein interaction analysis.

For further information please contact M. Boshart by email (boshart(at)lmu.de) or phone +49 89 2180 74600.

*Please note that this project is only available, if the PhD candidate is holder of a scholarship!

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Supervisor: Prof. Peter GEIGENBERGER (Plant Sciences, Biochemistry, Storage Metabolism)

Title: Regulation of plant metabolism in response to low oxygen concentrations

The main objective of this project is to identify and characterize signaling components that are involved in the proactive response of plants to low oxygen concentrations. Previous work was mainly focused on signaling components that are involved in the reprogramming of gene expression in response to low oxygen. It was found that in plants, the molecular response to hypoxia is triggered via the relocalisation of a constitutively expressed transcription factor (RAP2.12) from the plasma membrane to the nucleus. Subsequent fine-tuning of the activity of RAP2.12 is modulated via the destabilization of the protein via oxidation of the penultimate cysteine that prepares the protein for degradation via the N-end rule for proteosomal degradation. The main aim of the proposed project is the functional characterization these pivotal components of the oxygen sensing and signaling pathway in plants. The first objective is to investigate how the cellular redox status affects the cysteine oxidation that prepares the protein for degradation. The second objective is to investigate the impact of the oxygen sensor mechanism on the regulation of cellular redox status and respiratory metabolism.

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Supervisor: Prof. Kirsten JUNG (Microbiology, Cell Biology, Biochemistry)

Title: Dynamics of receptor localization

Adaptation and differentiation of bacterial populations is influenced by external cues. Key mediators of these processes are receptors that perceive extracellular information and transduce them to intracellular signalling networks resulting ultimately in a cellular response. The pH-sensor and transcriptional regulator CadC of Escherichia coli is a membrane-integrated receptor that also binds to the DNA. In addition, CadC forms a co-sensory complex with the membrane-integrated transporter LysP. We found that elongation factor P translationally regulates the copy number of the polyproline-containing pH-sensor CadC [Ude, S., Lassak, J., Starosta, A.L., Kraxenberger, T., Wilson, D.N. & Jung, K. (2013) Science 339, 82]. EF-P, a conserved protein in all bacteria and orthologous to archaeal and eukaryotic initiation factor 5A, rescues ribosome stalling at poly-proline sequences. The project focuses on the elucidation of the regulatory determinants and spatiotemporal dynamics to form and maintain the CadC/LysP as well as the CadC/DNA complexes and on the question how the RNA-polymerase is recruited under stress conditions.

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Supervisor: PD Dr. Stylianos MICHALAKIS (Gene Therapy, Neuroscience, Pharmacology, Epigenetics)

Title: Mechanisms of Neurodegeneration in hereditary blinding diseases

Inherited retinal degenerative disorders are characterized by the deterioration of the retinal function caused by the progressive cell death of light sensing photoreceptors. Unfortunately, the mechanisms involved in retinal degeneration are poorly understood. Thus, aim of this project is to investigate degenerative mechanisms in various kinds of hereditary blinding disease models by employing state-of-the-art biochemical, genetic, cell biological and viral gene transfer methods in combination with advanced in vitro and in vivo bioimaging (e.g. FRET, FLIM, OCT, cSLO) and functional analysis (e.g. ERG, vision-guided behavior).

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Supervisor: Prof. Joerg NICKELSEN (Plant Sciences, Biochemistry, Genetics)

Title: Regulation of chloroplast gene expression in Chlamydomonas

Due to the endosymbiotic evolutionary history of chloroplasts, most of the multimeric plastid protein complexes are formed by subunits which are encoded by either the nuclear or the chloroplast genome. This intrinsic complicated situation has led to the development of a coordination system for gene expression in both cellular compartments as well as a chloroplast biogenesis machinery that ensures the ordered step-wise assembly of photosynthetic complexes within the organelle. Moreover, both processes appear to be interlinked via feed-back control mechanisms that involve the sensing of non-assembled complex subunits. Accumulating evidence  indicate that numerous factors are involved in these regulatory processes. Some of which share characteristic motifs like e.g. TPR, PPR and other repeat domains or possess classical RNA binding domains and are typically organized in high-molecular weight complexes [Schwarz et al. (2007) Plant Cell 19: 3627-3639; Johnson et al. (2010) Plant Cell 22: 234-248]. This project aims at elucidating the molecular function of nucleus-encoded proteins potentially being involved in the biogenesis of thylakoid membranes in the model system Chlamydomonas reinhardtii.

Dependent on funding, the PhD position will be available by summer 2014.

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Supervisor: Prof. Martin PARNISKE (Genetics, Biochemistry, Cell Biology)

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 PhD 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.

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Supervisor: Prof. John PARSCH (Evolution, Functional Genomics)

Title: Population genomics and environmental adaptation in Drosophila ananassae

When organisms are faced with new environmental conditions, such those caused by climate change or range expansion, they must adapt in order to survive. However, it has been difficult to identify the specific genes and molecular mechanisms that underlie environmental adaption. Here we propose to investigate cold adaptation in the fruit fly Drosophila ananassae, a species that has recently expanded from its home range in tropical Asia to colonize temperate regions. We previously found that within a population of D. ananassae from Bangkok, Thailand, there is natural variation in cold tolerance, as measured by the time required for the flies to recover from a cold shock. The population otherwise does not show any sign of population structure, suggesting that the difference in cold shock recovery is determined by a small number of genes with large effects. Thus, D. ananassae is a promising model system for determining the genetic basis of cold adaptation. In this project, we will perform high-throughput gene expression analysis of multiple D. ananassae strains before, during and after cold shock. We will also survey genome-wide DNA sequence polymorphism in this species and use population genetic analyses to identify genes involved in cold tolerance and adaptation. The results of these experiments will shed light on thermal adaptation of natural populations. In addition, the use of state-of-the-art genomic methods will provide new information on genome-wide genetic polymorphism among D. ananassae strains, as well as divergence to the closely related species D. atripex. These data will not only facilitate the identification of genes and polymorphisms associated with adaptation to cold, but will also uncover genes that have been subject to recent and long-term adaptive evolution. In addition, the genomic data will allow us to test hypotheses regarding the evolution of sex-biased genes and sex chromosomes.

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Supervisor: PD Dr. Katrin PHILIPPAR/Prof. Juergen SOLL (Plant Sciences, Biochemistry, Molecular Biology)

The plastid organelle family conducts vital biosynthetic functions in every plant cell. First and foremost, chloroplasts carry out photosynthesis and thereby produce carbohydrates. However, the reduced carbon skeleton is used also for the plastid intrinsic biosynthesis of many other compounds such as isoprenoids, nucleic acids, amino acids, fatty acids, iron-sulfur clusters, or polyphenols. Nitrite produced in the cytosol during nitrate assimilation is transported into the plastid and reduced to ammonia by nitrite reductase. All subsequent reactions of primary assimilation and amino acid synthesis take place within plastids. These manifold biosynthetic functions thus require different selective transport mechanisms across both plastid envelope membranes. In consequence the proteins mediating these transport processes represent checkpoints for the control by metabolic signalling during the life of a plant cell.

Title: Function of plastid metabolite transporters and channels

The goal of this project is to understand how chloroplast envelope localized solute channels and transporters contribute to metabolic networking and signalling in the plant cell. This will be achieved by obtaining a detailed understanding of their properties, e.g. substrate specificity, regulation of gating and protein structure. The work program includes the detailed biochemical characterization of plastid metabolite transporters as well as physiological analysis of their integration into the signaling and metabolic network of the cell. We are using a combined approach of biochemical, genetic, transcriptomic, metabolomic, physiological and functional analysis. The latter involves electrophysiological approaches as well as transport studies in liposomes, E. coli and yeast cells. Plant model organisms are Arabidopsis thaliana for mutant and phenotype analysis and pea (Pisum sativum) for biochemical assays. The project will contribute to fundamental questions of plant membrane biology and physiology.

Review articles:

Pudelski, B., Schock, A., Hoth, S., Radchuk, R., Weber, H., Hofmann, J., Sonnewald, U., Soll, J., and Philippar, K. (2012). The plastid outer envelope protein OEP16 affects metabolic fluxes during ABA-controlled seed development and germination. J. Ex. Bot. 63, 1919–1936.

Pudelski, B., Kraus, S., Soll, J., and Philippar, K. (2010). The plant PRAT proteins – preprotein and amino acid transport in mitochandria and chloroplasts. Plant Biol. Sep. 12 (Suppl. 1), 42-55.

Duy, D., Soll, J., and Philippar, K. (2007). Solute channels of the outer membrane: from bacteria to chloroplasts. Biol Chem. 388, 879-889.

For further information see: http://www.botanik.bio.lmu.de/professuren/soll/ags/philippar/index.html

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Supervisor: PD Dr. Katrin PHILIPPAR (Plant Sciences, Biochemistry, Molecular Biology)

Plastids harbor many vital biosynthetic functions during growth and development. Thus, plastid metabolite synthesis requires solute exchange across the outer and inner envelope membranes. Because fatty acid synthesis in plants exclusively takes place in plastids, export for further lipid metabolism is required. However, knowledge on proteins involved in plastid export of fatty acids is still scarce.

We isolated FAX1 (fatty acid export 1), a novel membrane protein in the inner chloroplast envelope of Arabidopsis thaliana. FAX1 function is crucial for biomass production, male fertility, and synthesis of FA-derived compounds such as lipids, ketone waxes or pollen cell wall material. Whereas ER-derived lipids decrease when FAX1 is missing, levels of plastid-produced lipids increase. FAX1 over-expressing lines show the opposite behavior. Since in yeast, FAX1 could complement for FA-transport, we conclude that FAX1 mediates FA-export across the plastid inner envelope.

Title: Fatty acid transport in chloroplasts

The objective of the project is to describe the function of the FAX1-like proteins FAX2-FAX7. This will be achieved by obtaining a detailed understanding of their properties, e.g. expression pattern, subcellular localisation, function, and protein structure. The work program includes the detailed molecular and biochemical characterization of FAX-like proteins. We are using a combined approach of biochemical, genetic, transcriptomic, metabolomic, physiological and functional analysis. Plant model organisms are Arabidopsis thaliana for mutant and phenotype analysis and pea (Pisum sativum) for biochemical assays. Further a transfer to the oilseed crop Brassica napus is planned. Methods and approaches that will be used include subcellular localisation of proteins (in vivo GFP-targeting, in vitro protein import, immunoblot); protein interaction studies in vitro (yeast hybrid) and in vivo (BiFC, immuno-precipitation); biochemical analysis of membrane protein complexes; genetic, physiological and morphological characterisation of mutant lines; DNA microarray analysis and quantitative RT PCR; as well as functional analysis of fatty acid transport in yeast cells.The project will contribute to fundamental questions of plant fatty acid as well as lipid transport and metabolism.

For further information see: http://www.botanik.bio.lmu.de/professuren/soll/ags/philippar/index.html

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Supervisor: Dr. Serena SCHWENKERT/Prof. Juergen SOLL (Plant Sciences, Biochemistry, Molecular Biology)

In the eukaryotic cell most organellar proteins are synthesized as preproteins in the cytosol and are post-translationally transported to chloroplasts or mitochondria. Our group is specifically interested in cytosolic factors such as molecular chaperones, protein kinases and phosphatases, which are indispensable for efficient preprotein import into the organelles.

Title 1: Function of preprotein phosphorylation in organellar biogenesis

Organelle biogenesis is highly regulated at the transcriptional, translational and posttranslational level dependant on the developmental stage of the organism, its organ differentiation as well as in response to internal and external (environmental) stimuli. Posttranslational phosphorylation of preproteins directed to chloroplasts by cytosolic protein kinases regulate their transport efficiency. In addition, protein phosphatases are also involved in influencing kinase activity as well as transport competence of preproteins. Therefore these enzymes represent important steps in the regulatory circuits controlling organelle biogenesis.

The doctoral project will elucidate in detail how these kinase and phosphatase enzymes act in a cellular and organismic context, using genetic, biochemical, structural and in vivo approaches. This will yield important contributions to fundamental questions in cell biology on organellar biogenesis and the signaling networks between organelles and the nucleus controlling it.

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Title 2: Cytosolic chaperone function in organellar preprotein import

During posttranslational protein transport the preproteins have to kept in an import competent state and molecular crowding has to be prevented, since this can easily lead to misfolding or aggregation. This process is assisted by the molecular chaperones HSP90 and HSP70, which act in concert with a number of co-chaperones. The chaperone associated preproteins can interact with special docking proteins on the organellar surfaces and be subsequently transferred to the import apparatus.

In this project we will apply a variety of biochemical and molecular biological techniques, such as protein purification, co-immunoprecipitation and expression of fluorescent proteins to characterize the molecular and regulatory function of chaperones during posttranslational protein transport. The functional and structural analyses of these docking proteins will not only provide insight into the import mechanism of preproteins but also elucidate the role of chaperones and the respective receptors in specific targeting of preproteins.

Review article: Schwenkert, S., Soll, J., and Bölter, B. 2011. Protein import into chloroplasts-How chaperones feature into the game. Biochim Biophys Acta. 1808, 901-911.

For further information see: http://www.en.botanik.bio.lmu.de/research/soll/subgroups/schwenkert/index.html

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