LSM doctoral projects

Please note:

National and international candidates are welcome to apply
You have to apply through our online application tool which is open until 30 November 2022, 12:00 noon CET!
For further information about the projects, feel free to contact the supervisor directly
All offered projects are financed by third-party funds of the supervisor (e.g. DFG funded)
The funded projects below cover most areas of natural and life sciences from Cell and Developmental Biology, Genetics, Microbiology, and Plant Sciences.
On the online application tool, three projects can be selected.
You are welcome to browse through our faculty members´research here
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Research groups

Prof. Dr. Kirsten Jung (Microbiology)
Title: Acidification of the cytoplasm as a poorly understood stimulus for the activation of stress adaptation in Escherichia coli

Description:

On Earth, there are many habitats with low pH, such as the gastrointestinal tract of vertebrates or areas with acidic soils. Although most bacteria are neutralophiles, they are able to survive in acidic environments. Acid stress sensing and adaptation allow these bacteria to maintain a constant intracellular pH under moderate acid stress.
In our preliminary work, we exposed Escherichia coli to different degrees of acid stress, and measured the changes in synthesis rates of all proteins using RiboSeq. We found that the intracellular pH of E. coli decreases by about one pH unit under strong acid stress, which significantly affects the protonation states of all biological molecules and influences their charge, conformation and function. It will be the aim of the project to identify and characterize proteins that undergo translational regulation under strong acid stress. Their contribution to acid stress survival will be studied. In addition, the interconnectivity between acid stress response and antibiotic resistance will be investigated.

Qualifications:
Experience with microbiological techniques, e.g., construction of mutants and reporter strains, and molecular and biochemical techniques, e.g., purification and characterization of RNA and proteins, is required.

References:
Brameyer, S., Schumacher, K., Kuppermann, S., Jung, K. (2022) Division of labor and collective functionality in Escherichia coli under acid stress. Commun. Biol. 5: 327.

Prof. Dr. Michael Kiebler (Cell Biology)
Title: Ribonucleoprotein (RNP) particle assembly

The Department of Cell Biology – Anatomy III at the LMU Biomedical Center is looking for a motivated and dedicated PhD student (PhD, Dr. rer.nat) to biochemically characterize RNA Protein complexes. In the proposed DFG project, we want to study ribonucleoprotein (RNP) particle assembly in primary neurons and unravel the underlying dynamics of the RNP network. Here, we will exploit a battery of interactor screens complemented with state-of-the-art biochemistry and live-cell imaging to unravel how the RNA-binding protein (RBP) network dynamically assembles and balances physiological alterations in the cell.

Numerous interdisciplinary methods will be used in the project, from experiments with primary neurons, including FISH, luciferase and GFP assays, qPCR, BioID and APEX biochemistry to virus production, transduction and sample preparation. Experience in these methods is of advantage. An existing bioinformatics background is recommended.
The candidate (m/f/d) should hold a M.Sc. degree (or equivalent) and be an enthusiastic and highly motivated student who can work independently in a team. The ideal candidate will join an international research group in a highly dynamic working environment (with English as the main written/spoken language) and is expected to be reliable, responsible and have high scientific standards.

The position is limited to 3 years (TV-L 65% E13).

Further informationen: https://www.zellbio.anatomie.med.uni-muenchen.de/index.html

Please send an email with your CV, letter of motivation and two contacts of reference in one single pdf file to
Bewerbungsadresse:
Dr. Barbara Nitz
Biomedizinisches Centrum
Ludwig-Maximilians-Universität München
LS Zellbiologie (Anatomie III)
Großhaderner Str.9, 82152 Planegg-Martinsried
Barbara.Nitz@bmc.med.lmu.de

Prof. Dr. Andreas Klingl (Plant Sciences)
Title: A comparative approach to the 3-dimensional structure of the plantmicrobe interface using FIB/SEM tomography

Description:

Several recent studies dealing with the interaction of plants with microorganisms (beneficial or pathogenic; Parniske, 2000) highlighted the importance and the role of the so-called plant-microbe interface (PMI), e.g. the haustorium, a structure that is produced by plant pathogenic oomycetes and fungi (Bozkurt and Kamoun, 2020). It contains membranes (Limpens, 2019), receptors and other important players. It could also, be indicated that a 3-dimensional visualization of the PMI could have a very high potential for a better understanding of the underlying mechanisms (Ivanov et al., 2019; Roth et al., 2019). With the access to a multitude of mutualistic and parasitic symbiosis of plants and microbes, we want to illustrate common features and significant differences.

After chemical (Cerri et al., 2017; Liang et al., 2019) or cryo-fixation (high-pressure freezing (HPF); Rachel et al., 2010) of the respective sample material, we will perform TEM and STEM tomography (Walther et al., 2018) and FIB/SEM tomography (e.g. Luckner and Wanner, 2018a, b), which will be followed by image analysis, segmentation and the generation of 3D-models using the AMIRA software package.

In our study, we are going to use wild type hosts and mutualistic and parasitic symbiosis with microbes to investigate the following host-microbe interaction scenarios: arbuscular mycorrhiza (AM) in tomato, Phytophtora in tomato, nitrogen fixing root nodules by actinobacteria Frankia (actinorhizal symbiosis), rhizobia in legumes, downy mildew (Hyaloperonospora arabidopsidis) in Arabidopsis thaliana, white rust (Albugo laibachii) in A. thaliana and powdery mildew infection of barley and Arabidopsis thaliana.

To facilitate the recognition of the region of interest (ROI), all those approaches will be supported by assisted by correlative light and electron microscopy (CALM).

Methods:

Cryo electron tomography (cryo-ET)
Transmission electron microscopy (TEM)
High-pressure freezing
3D electron microscopy
FIB/SEM-tomography

References:
Bozkurt, T.O., and Kamoun, S. (2020). The plant-pathogen haustorial interface at a glance. J. Cell Sci. 133:
jcs237958. doi: 10.1242/jcs.237958
Cerri, M.R., Wang, Q., Stolz, P., Folgmann, J., Frances, L., Katzer, K., Li, X., Heckmann, A.B., Wang, T.,
Downie, A., Klingl, A., de Carvalho-Niebel, F., Xie, F., and Parniske, M. (2017). The ERN1 transcription factor
gene is a target of the CCaMK/CYCLOPS complex and controls rhizobial infection in Lotus japonicus. New
Phytol. 215(1): 323-337. doi: 10.111/nph.14547
Ivanov, S., Austin II, J., Berg, R.H., and Harrison, M.J. (2019). Extensive membrane systems at the hostarbuscular
mycorrhizal fungus interface. Nat. Plants 5: 194-203. doi: 10.1038/s41477-019-0364-5.
Liang, J., Klingl, A., Lin, Y.Y., Boul, E., Thomas-Oates, J., Marín, M. (2019). A sub-compatible rhizobium strain
reveals infection duality in Lotus. J. Exp. Botany 70(6):1903-1913. doi: 10.1093/jxb/erz057
Limpens, E. (2019). Extracellular membranes in symbiosis. Nat. Plants 5: 131-132. doi: 10.1038/s41477-019-
0370-7
Luckner, M., and Wanner, G. (2018a). From light microscopy to analytical SEM and FIB/SEM in biology: fixed
coordinates, flat embedding, absolute references. Microsc. Microanal. 24(5): 526-544. doi:
10.1017/S1431927618015015
Luckner, M., and Wanner, G. (2018b). Precise and economic FIB/SEM for CLEM: with 2 nm voxels through
mitosis. Histochem. Cell Biol. 150(2): 149-170. doi: 10.1007/s00418-018-1681-x
Parniske, M. (2000). Intracellular accommodation of microbes by plants: a common developmental program for
symbiosis and disease? Curr. Opin. Plant Biol. 3: 320-328.
Rachel, R., Meyer, C., Klingl, A., Gürster, S., Heimerl, T., Wasserburger, N., Burghardt, T., Küper, U.,
Bellack, A., Schopf, S., Wirth, R., Huber, H., and Wanner, G. (2010). Analysis of the ultrastructure of archaea
by electron microscopy. Method. Cell Biol. 96: 47-69.
Roth, R., Hillmer, S., Funaya, C., Chiapello, M., Schumacher, K., Lo Presti, L., Kahmann, R., and
Paszkowski, U. (2019). Arbuscular cell invasion coincides with extracellular vesicles and membrane tubules. Nat.
Plants 5: 204.211. doi: 10.1038/s41477-019-0365-4.
Walther, P., Bauer, A., Wenske, N., Catanese, A., Garrido, D., Schneider, M. (2018). STEM tomography of
high-pressure frozen and freeze-substituted cells: a comparison if image stacks obtained at 200 kV or 300 kV.
Histochem. Cell Biol. 150(5): 545-556. doi: 10.1007/s00418-018-1727-0.

Prof. Dr. Dario Leister (Plant Sciences)
Title: Enhancing photosynthesis by synthetic biology and adaptive laboratory evolution

Description:

In this project, parts of the light reactions of photosynthesis from very different species will be combined in a model cyanobacterium by genetic engineering. The goal is to enhance photosynthesis with respect to its potential to use light from different wavelengths. In a complementary approach we use adaptive laboratory evolution to make photosynthetic organisms more tolerant against different stresses like for instance high light or high temperature stress. Corresponding mutations will be identified by whole-genome sequencing, characterized for their molecular effects, and tested for their potential to enhance stress tolerance in several species.

Prof. Dr. Dario Leister (Plant Sciences)
Title: Acclimation to fluctuating light: cyclic electron flow

Description:

Light intensities fluctuate under natural conditions. Thus, proper regulation of photosynthesis is pivotal for effective plant performance under fluctuating light (FL). Cyclic electron flow (CEF) involves the two thylakoid membrane proteins PGR5 and PGRL1, both of which are crucial for plant development under FL. Multiple lines of evidence indicate that PGR5 and PGRL1 form a complex in the thylakoid membrane. However, the precise mechanism of their action, the regulation of corresponding activities and whether this process has the potential for enhancing acclimation to FL are elusive. In preparatory work, we showed that PGR5 and PGRL1 can rebuild CEF in the cyanobacterium Synechocystis sp. PCC 6803, making it now possible to study PGR5-dependent CEF in a prokaryote employing superior genetic tools in relatively short time spans. Moreover, we found that the pgrl2 mutation suppresses the pgrl1 mutation but not the pgr5 mutation - or in other words: PGR5 can function without PGRL1. This result significantly revised our view on PGR5-dependent CEF with PGR5 being the central component that is regulated by PGRL1 and PGRL2.
In this project, we will characterise suppressor mutations of prg5 and pgrl1 at the genetic, physiological and protein level. In addition to the model plant Arabidopsis thaliana, we will employ our cyanobacterial test system with reconstructed PGR5-dependent CEF to rapidly perform molecular and mechanistic studies.

Dr. Macarena Marín (Genetics)
Title: Tissue-specific regulation of lipid polyester synthesis genes controlling oxygen permeation into Lotus japonicus nodules

Description:

Symbiotic nitrogen fixation reduces the dependency on costly and environmentally hazardous synthetic nitrogen fertilizers. The rhizobia nitrogenase that catalyses the reduction of atmospheric nitrogen into ammonia is oxygen sensitive. Legumes protect the nitrogenase by creating a microaerophilic environment inside nodules. A long-standing model posits that oxygen diffusion into nodules is limited by a barrier in the nodule periphery. By exploring the natural diversity of Lotus japonicus accessions using comparative transcriptomics, we identified genes involved in the deposition of lipid polyesters on cell walls that are specifically expressed in the nodule periphery. Spatiotemporal analysis of promoter activity controlling the expression of two Fatty acyl-CoA reductases (FARs) genes showed distinct activation in the root and nodule endodermis. Mutant lines in one of these genes, showed an increase in nodule permeability, higher oxygen concentrations inside nodules, impaired nitrogenase activity, and reduced shoot growth. This supports a model in which nodule-specific lipid polyester synthesis genes mediate the formation of a permeation barrier in the nodule periphery. In this project we will investigate the function and regulation of these genes, as they are promising molecular markers for the establishment of this nodule barrier. To this end we will create mutant lines by CRISPR/Cpf1 gene editing and phenotypically characterize them, we will generate reporter lines to determine the ontogeny of the nodule barrier, and will investigate the regulation of FAR genes at a molecular level. This work will advance our understanding of how the nodule barrier is formed, a key adaptation enabling nitrogen fixation in legumes.

Contact information:
If you are interested in this project, contact Macarena Marin

Prof. Dr. Markus Meissner (Experimental Parasitology)
Title: Analysis of Epigenetic Regulation in Plasmodium

Description:

The research group of Prof. Markus Meissner (LMU), in collaboration with Prof. Gernot Längst (University of Regensburg) invites applications for doctoral student positions to work on fundamental biological aspects of apicomplexan parasites and their host cells. A major focus will be the analysis of gene regulation and host cell egress of Plasmodium falciparum, the causative agent of malaria.
The malaria causing parasite Plasmodium falciparum (Pf) is an unicellular eukaryote with a complex life cycle between human host and mosquito vector. Each life cycle stage can be characterised by a specific transcriptional profile, suggesting a complex transcriptional regulation mechanism. The parasite is unique, having the AT-richest genome sequenced to date, the most divergent histone proteins in the eukaryotic domain, resulting in a lack of global nucleosome positioning and exhibiting a 10-fold reduction in number of transcription factors, when compared to organisms of similar complexity. Therefore, it is not understood how the tightly regulated gene expression profile during developmental stage transition is established. It is suggested that the regulation of the gene expression cascade depends on epigenetic mechanisms involving nucleosome remodeling.
In contrast to other eukaryotes, Pf has a non-redundant set of chromatin remodeling enzymes. This allows to study the function of individual classes of chromatin remodelers in the cell, by inducible knockout systems and associated functional studies. We chose the ISWI-type enzyme pfSnf2L, created inducible knockout parasite lines , and show that pfSnf2L is an essential enzyme for parasite survival. Conditional deletion of pfSnf2L results in parasites unable to exit the erythrocyte. In good agreement, gene expression analysis demonstrates that exportome genes are not activated during the intraerythrocytic stage of the parasite. This conditional mutant will allow us to address the effects of pfSnf2L on chromatin structure and gene regulation during the erythrocyte life cycle of Pf. The study is combined with the functional characterization of the recombinant pfSnf2L enzyme, to draw a mechanistic picture of the cellular chromatin changes. We aim will unravel the mechanism of chromatin remodeling and nucleosome positioning on gene expression networks and phenotypical changes of Plasmodium falciparum.

The Meissner lab is based in the Faculty of Veterinary Medicine. Numerous core facilities ensure state of the art equipment and expertise.
Information relating to our research is available on our webpage https://www.en.para.vetmed.uni-muenchen.de/index.html

For representative studies of the Meissner lab see:
Li, W., et al., Nat Microbiol, 2022. 7(6): p. 882-895.
Periz, J., et al., Nat Commun, 2019. 10(1): p. 4183.
Gras, S., et al., PLoS Biol, 2019. 17(6): p. e3000060.
Stortz, J.F., et al., BioRxiv, 2018: p. 488528.
Andenmatten, N., et al., Nat Methods, 2013. 10(2): p. 125-7.

Prof. Dr. Martin Parniske (Plant Genetics)
Title: Sequence adaptations in the symbiosis receptor-like kinase (SymRK) enabeling nitrogen-fixing root nodule development

Prof. Dr. Martin Parniske (Plant Genetics)
Title: Spatio-temporal dynamics in the composition and function of the CCaMK/CYCLOPS complex, the master regulator of plant root symbioses

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 candidate will study the relevance of the identified additional complex components using a range of techniques, including reverse genetics utilizing transposon insertion populations and/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.

Prof. Dr. Martin Parniske (Plant Genetics)
Title:Harnessing natural genetic resources to defend fruit plants against insect attack (in collaboration with Nicolas Gompel)

Drosophila suzukii, a member of the vinegar fly family, has become the most damaging pest worldwide for a wide variety of soft fruits. While other Drosophila species lay their eggs into decaying fruits, D. suzukii has evolved the ability to insert eggs into the flesh of ready-to-harvest ripe fruits either on plants or in storage. Hatched larvae then consume the fruits from inside out and infected fruits are no longer suitable for human consumption. Aiming for a sustainable and effective control method, we utilized a diverse collection of strawberry plants (genus Fragaria) and identified sources of natural resistance to D. suzukii, the first-reported herbivore resistance in fruits. Preliminary results indicate inhibitory effect at early stages of D. suzukii larvae development and involvement of plant secondary metabolites. As a consequence, resistant genotypes do not support proliferation of flies, hence limiting the source of infestation. In this project we aim to understand the genetic, molecular and metabolic mechanisms underpinning this resistant phenotype. We team up with strawberry breeding experts to approach the ultimate goal of transferring the resistance to commercial strawberry cultivars. In the long term we aim to identify the genes and mechanisms underlying this resistance and thus provide alternative strategies for the production of healthy fruits that can replace insecticide application.

Prof. Dr. Christof Osman (Cell Biology)
Title: The interplay between mitochondrial genome integrity and mitochondrial physiology in heteroplasmic cells (collaboration with Dr. David Hörl)

Mitochondria are known as the power plants of the cell because they supply the cell with energy through a process known as oxidative phosphorylation. Essential subunits of the complexes responsible for this process are encoded by the mitochondrial genome (mtDNA). mtDNA is present in multiple copies within cells and these copies are distributed throughout the mitochondrial network. Given the fundamental importance of mtDNA in cellular energy supply, it is critical that cells combat accumulation of mutant mtDNA copies to ensure maintenance of a healthy pool of mtDNA copies. Remarkably, we could previously show that the single-celled model organism S. cerevisiae can distinguish between intact and mutant mtDNA copies and promote generation of progeny containing predominantly intact mtDNA. However, it remains unknown, how cells determine mtDNA quality to eventually facilitate propagation of intact over mutant mtDNA copies. In this project we aim to address this question by using advanced microscopy techniques and image analysis. In particular, we aim to understand the spatial link between mtDNA quality and mitochondrial physiology. This project will be conducted in close collaboration between the Osman lab and Dr. David Hörl and will combine expertise in cell biological approaches, microscopy and image analysis.

Qualifications:
Experience with molecular and cell biological techniques, microscopy and basic programming.

References:
Jakubke C.*, Roussou R.*, Maiser A., Schug C., Thoma F., Bunk D., Hörl D., Leonhardt H., Walter P., Klecker T. & Osman C. (2021) Cristae-dependent quality control of the mitochondrial genome. Science Advances, Vol 7, Issue 36
Bunk D., Moriasy J., Thoma F., Jakubke C., Osman C. & Hörl D. (2022) YeastMate: Neural network-assisted segmentation of mating and budding events in S. cerevisiae, Bioinformatics, Vol 38, Issue 9

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