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DAAD-LSM doctoral projects

Please note:

  • Only international applicants, who have not been in Germany longer than 15 months by the end of February 2023 are eligible for the DAAD-GSSP scholarship !
  • 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
  • The offered projects of this DAAD-GSSP application cover most areas of natural and life sciences from Cell and Developmental Biology, Genetics, Ecology, Microbiology, Molecular Biology, Biochemistry, Evolutionary Biology, Plant Sciences, Pharmacology and Systematic Botany and Mycology.
  • On the online application tool, three projects can be selected.
  • You are welcome to browse through our faculty members´research here
Research groups
Title: Induction of defence compounds in rice by fungal elicitors
Project description:
Plants mostly grow in dense communities, together with plants from the same or a different species. Because resources are scarce, plants must compete with their neighbours for nutrients, space, and water. Some plant species, including important crops such as rice, release chemical compounds to inhibit the growth of neighbours and to defend themselves against various pests.

Upon perceiving a chemical trigger, rice plants produce and release a particular type of diterpenes, momilactone A and B, that act against fungal pathogens as well as against non-kin plant species (Serra Serra et al. 2021). In this project, our goal is to identify the molecular trigger(s), the mechanism by which they are perceived, and the signalling cascade that ultimately leads to the enhanced production and release of the compounds. To this end, we employ a combination of genetics, genomics, biotechnology, and metabolomic analyses. In collaboration with microbiologists and biochemists, we will test an array of fungal extracts and filtrates from both beneficial and pathogenic fungi; via iterative fractionations and purifications, we aim to identify the specific molecules that trigger the response. Using reporter lines, mutant collections, and CRISPR/Cas9 technology, we will then focus on identifying the components of the signalling cascade.

The project is embedded in a group with very diverse expertise, ranging from Bioinformatics and Genomics to Plant Genetics and Biochemistry. We are looking for candidates with a solid background in molecular biology and genetics; expertise in computational data analysis and/or plant biology is a plus. Candidates should have an advanced level in spoken and written English. For further information, please contact Dr. Claude Becker.
 Prof. Dr. Thorben Cordes (Physical and Synthetic Biology)
Title: ABC importers as targets for antibiotics of pathogenic bacteria
Collaborative Project: Kirsten Jung (Microbiology)
Multidrug resistant bacteria and lagging development of novel antibiotics were the cause of >17 million deaths in 2006.1 As pointed out by the world health organization (WHO) new strategies against drug resistant bacterial infections are urgently required ( Bacterial ATP Binding Cassette (ABC) import systems have a huge potential as targets for antibiotic development due to their involvement in a numerous biological processes, their extracellular localization and the absence of homologous proteins in the mammalian hosts.2 These transmembrane systems transport wide variety of substrates ranging from sugars and peptides to metal ions, osmolytes and vitamins by utilizing the energy from ATP-hydrolysis. Different studies have shown that certain ABC importers are involved in bacterial virulence or survival in the host organism.2 Here, we propose to disable the periplasmic or extracellular components of ABC import systems, substrate binding domains or proteins (SBPs). They initiate substrate transport via its delivery to the membrane-embedded ABC import system allowing selective and ATP-coupled transport. In the framework of this project, you will conduct a structural analysis of the selected SBPs, establish and optimize the methods for protein expression, purification and fluorophore labelling of the target SBP and test the established fluorescence assays using single-molecule3, bulk- and high-throughput fluorescence detection methods. Furthermore, you will identify SBP inhibitors in silico, test and optimize their ability to bind the relevant SBPs in biochemical experiments. Finally, in collaboration with the lab of Kirsten Jung, you will test the impact of promising inhibitor molecules on the growth and infectivity of bacteria.
For more information visit our webpage

1. Martens, E.; Demain, A. L., The antibiotic resistance crisis, with a focus on the United States. The Journal of antibiotics 2017, 70 (5), 520-526.
2. Garmory, H. S.; Titball, R. W., ATP-binding cassette transporters are targets for the development of antibacterial vaccines and therapies. Infection and immunity 2004, 72 (12), 6757-6763.
3. de Boer, M.; Gouridis, G.; Vietrov, R.; Begg, S. L.; Schuurman-Wolters, G. K.; Husada, F.; Eleftheriadis, N.; Poolman, B.; McDevitt, C. A.; Cordes, T., Conformational and dynamic plasticity in substrate-binding proteins underlies selective transport in ABC importers. eLife 2019, 8, e44652.


Prof. Dr. Laurent Frantz (Palaeogenomics)
Title: Understanding animal domestication using palaeogenomics

Animal domestication was one of the most important transitions in human history, beginning with the long-term association between hunter–gatherers and wolves more than 15,000 years. This long term association with people resulted in new selective pressures which led to substantial biological changes in animal species (e.g. behavior, appearance, circadian rhythm etc.), as well as in people (e.g. via spread of zoonotic disease etc).

Genomic data obtained from modern domestic animals can be used to address questions about the geographical and temporal origins as well as to understand the strength and consequences of these selective pressures on the genome. Genomic information obtained from living animals, however, provides only a contemporary snapshot of a long-term evolutionary process. Domestic species have also dramatically changed in less than a century, e.g. chicken growth rate has tripled in the last 50 years and cranial shape variation across modern dog breeds now exceeds the range of differences observed across the entire order of Carnivora. This makes it difficult to make inferences about domestication based solely on the analyses of modern population data.

In the past decade, novel molecular techniques have enabled access to genetic information from past populations (palaeogenomics). This has allowed us to obtain genomes of animals and that of the pathogens they were infected with, using DNA extracted from ancient skeletal remains, found at archeological and palaeontological sites. Palaeogenomics allows us to generate genomic time series, and answer questions related to the origin and the spread of domestic populations across the globe, to assess how animals adapted to the myriad of environments in which they were introduced, or to better understand ancient events of zoonoses.

The student will be integrated in our team based at LMU and London, and will be expected to take part in international collaborative networks, including with groups in Oxford, the NIH, and UCL (among others). They will be given the opportunity to choose one of multiple specific projects focusing on the evolutionary history of domestic species and that of their pathogens. This includes, projects related to the temporal and geographic origin of domestic dogs, the process of fertilization in pigs (i.e. what happened to genome when species go back to the ‘wild’), or the study of the evolution of pathogenic species that affect both animals and people (e.g. evaluate the role of domestic pigs as zoonotic pathogen reservoirs in the past).

Selected publications from our group:
1. Bergström, A. et al. (2022) ‘Grey wolf genomic history reveals a dual ancestry of dogs’, Nature, 607(7918), pp. 313–320.
2. Frantz, L.A.F. et al. (2020) ‘Animal domestication in the era of ancient genomics’, Nature reviews. Genetics, 21(8), pp. 449–460.
3. Bergström, A. et al. (2020) ‘Origins and genetic legacy of prehistoric dogs’, Science, 370(6516), pp. 557–564.
4. Feuerborn, T.R. et al. (2021) ‘Modern Siberian dog ancestry was shaped by several thousand years of Eurasian-wide trade and human dispersal’, PNAS, 118(39).
5. Plassais, J. et al. (2022) ‘Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids’, Current biology: CB, 32(4), pp. 889–897.e9.
6. Perri, A.R. et al. (2021) ‘Dog domestication and the dual dispersal of people and dogs into the Americas’, PNAS, 118(6).
7. Frantz, L.A.F. et al. (2019) ‘Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe’, PNAS 116(35), pp. 17231–17238.
8. Ollivier, M. et al. (2018) ‘Dogs accompanied humans during the Neolithic expansion into Europe’, Biology letters, 14(10).
9. Ní Leathlobhair, M. et al. (2018) ‘The evolutionary history of dogs in the Americas’, Science, 361(6397), pp. 81–85.
10. Frantz, L. et al. (2016) ‘The Evolution of Suidae’, Annual review of animal biosciences, 4, pp. 61–85.
11. Frantz, L.A.F. et al. (2016) ‘Genomic and archaeological evidence suggest a dual origin of domestic dogs’, Science, 352(6290), pp. 1228–1231.
12. Frantz, L.A.F. et al. (2015) ‘Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes’, Nature genetics, 47(10), pp. 1141–1148.

Prof. Dr. Ferraz  (Biology of Reproduction)
Title: Creating a testis-on-a-chip to investigate the effects of microplastics on male fertility


Reproduction is central to the capacity for species to maintain stable, healthy populations. Simply, if life can not reproduce, it will cease to exist. Over the past several decades, there has been a shift towards a “throw-away society” that is characterised by the excessive consumption of short-lived and single-use products, and a concomitant accumulation of environmental pollution and toxicants. Over this same timespan, there has been an alarming increase in the rates of reproductive dysfunctions and gamete abnormalities, reductions in gamete production, and altered embryo development in humans, animals and plants. This poor reproductive health not only reduces individual fecundity but, if widespread, species survival. While humans have introduced numerous pollutants that can impair reproductive systems, the potential impacts of microplastics (MPs) are of particular concern. Emerging studies are showing that MPs represent a potentially serious threat to the reproductive health of terrestrial species. Our lab has recently discovered the presence of MPs in seminal plasma and follicular fluid, and that MPs impact both female and male gametes in vitro.

To better understand the impact of MPs on male fertility, this project will combine bio-printing with microfluidics to develop an in vitro testis-on-a-chip model to study the effects of different microplastics particles on spermatogenesis and sperm function.

Please contact Prof. Ferraz for more information.

Dr. Sonja Grath (Evolutionary Biology/Ecology)
Title: O brother, where art thou? - Modelling the evolution of parthenogenesis

We are generally interested in the evolution of genetic and epigenetic mechanisms that determine sex-specific gene regulation. Animals display a wide variety of reproductive modes. While sexual reproduction is widespread and well-known, with this project, we aim to better understand the evolution of reproductive modes where males are actually absent. We will use mathematical modelling to understand different forms of parthenogenesis. Under which circumstances can this form of reproduction evolve and be maintained? In arthropods, parthenogenesis can be induced by endosymbionts such as Wolbachia that can perform different reproductive manipulations on its hosts. One example is cytoplasmic incompatibility (CI) where Wolbachia manipulates the sperm of infected males. When mated with an uninfected female, or a female harboring a different and incompatible strain of Wolbachia, the manipulated sperm leads to partial or even complete incompatibility with the female's eggs and induces lethality of the offspring by disrupting the development of the embryo. If the female however does carry the same Wolbachia infection and Wolbachia is also present in her eggs, the manipulation can be rescued, allowing for viable offspring to be produced. Previously, we developed a mathematical model to study under which circumstances CI can spread between and maintained in populations of oak gallwasps. In this project, we now want to extend and generalize this model to additional species, parameters and reproductive manipulations.
Given a sincere interest in molecular and evolutionary mechanisms, the project is also well suited for graduates from disciplines outside biology, such as mathematics, physics or computer science. Just get in contact with the principal investigator in case you have any questions.
Contact information:
For further information, please contact Sonja Grath

van der Kooi, C. J., Matthey-Doret, C., Schwander, T. (2017). Evolution and comparative ecology of parthenogenesis in haplodiploid arthropods. Evolution Letters 1-6: 304–316.

Werren, J. H., Baldo, L., & Clark, M. E. (2008). Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol, 6(10), 741-751.

Prof. Dr. Marc Gottschling (Systematic Botany and Mycology)
Title: Evolutionary origin and distribution of Bavarian freshwater dinoflagellates

Precise distribution data are necessary to explain the historical biogeography of organisms and to uncover the evolutionary mechanisms that have shaped their diversification, but also to predict future developments in a drastically changing world. The distribution of microorganisms, such as the ecologically and economically important group of unicellular dinophytes, reflects their dispersal ability and potential to establish new populations. Data on the distribution of these organisms, however, are both sparse and outdated. Molecular methods (including high throughput sequencing) have become the tool of choice to resolve identification issues. The successful candidate will inventory freshwater dinophyte species compositions of some 50 lakes in Bavaria, using rRNA amplicon sequencing. Bavaria has 382 lakes >1 ha that show a broad range of environmental parameters. Most lakes originated after the last ice age about 10-12.000 years ago. The group has multiple annual dinoflagellate morphology-based microscopic records (54 of them from research at the LMU Limnological Research Station Seeon). Phylogenies show that freshwater dinophytes segregate into distantly related lineages, and their molecular diversity is much better explored than their geographic occurrence. Dinophyte communities and their correlations with environmental parameters will be analysed with modern multivariate statistical methods, and the Bavarian ribotypes will be placed in a phylogenetic context using maximum likelihood methods. Bavarian dinoflagellates will also be considered in the European context using GenBank and the in-group sequence database of multiple spatially referenced accessions. The project will result in better knowledge about the spatial distribution and phylogenetic diversity of German dinophytes, will provide the first modern distribution maps for key species and is the basis for assessing the impact of climate change and acidification on freshwater dinophytes.

Selected publications
Gottschling M, J Chacón, A Žerdoner Čalasan, St Neuhaus, J Kretschmann, H Stibor & U John* (2020): Phylogenetic placement of environmental sequences using taxonomically reliable databases helps to rigorously assess dinophyte biodiversity in Bavarian lakes (Germany). Freshw Biol 65: 193–208.

Kretschmann J, A Žerdoner Čalasan, W-H Kusber & M Gottschling* (2018): Still curling after all these years: Glenodinium apiculatum Ehrenb. (Peridiniales, Dinophyceae) repeatedly found at its type locality in Berlin (Germany). Syst Biodivers 16: 200–209.

Žerdoner Čalasan A, J Kretschmann & M Gottschling* (2019): They are young, and they are many: Dating freshwater lineages in unicellular dinophytes. Environ Microbiol 21: 4125–4135.


Prof. Dr. Dr. Christian Grimm (Pharmacology and Toxicology)
Title: Novel endolysosomal transportome/channelome components in health and disease

Current State of Relevant Research

Cells are the elementary units of all life. Each cell contains numerous organelles that are essential for proper cell function, e.g. ribosomes for RNA into protein translation, a Golgi apparatus for protein modification, or mitochondria for energy production. One organellar machinery that is both essential for intracellular trafficking and degradation but also serves as an important signaling hub is the endolysosomal system. Endolysosomes are key for human health and disruption of endolysosomal function including its central role in intracellular Ca2+ signaling is strongly associated with disease pathology, affecting or causing neurodegenerative and lysosomal storage diseases, cancer and immunological diseases, metabolic, lung, or infectious diseases. The seemingly complex interaction between endolysosomes but also with other organelles raises the fundamental, yet largely unanswered question in cell biology of how a precise regulation of this intracellular communication and interaction network is achieved. Decoding the intracellular signaling pathways governing endolysosomal communication is critical not only for an in-depth understanding of cell biology
but also for the many disease pathologies endolysosomal dysfunction is associated with. Aim of this project is to decipher molecular components in mammalian cells that are necessary to tightly coordinate intracellular, in particular endolysosomal transport and communication, postulating that a distinctive set of endolysosomal cation channels/transport proteins are key to these processes. To address this aim, we will apply in vitro and in vivo models, novel techniques in cell biology, subcellular imaging, proteomics, bioinformatics and biophysics (i.e.,
endolysosomal patch clamp electrophysiology).

Peliminary Work Directly Relating to the Research Program

Members of the TRP family of mostly non-selective cation channels, the so called TRPML channels and the related two-pore channels (TPCs) which all reside in endolysosomes have been in depth investigated and characterized in the past. Yet, additional components of the endolysosomal transportome/channelome require further investigation, so do the numerous postulated interaction partners of TPCs and TRPMLs.

Specific Aims
Aims of the projects are
1) to characterize novel interaction partners of TPCs and TRPMLs in endolysosomes using endolysosomal patch-clamp electrophysiology and calcium imaging
2) to characterize additional components of the endolysosomal transportome/channelome
3) to identify novel, currently enigmatic components of the endolysosomal transportome/ Channelome



 Prof. Dr. Heinrich Jung (Microbiology)
Title: Transport and regulation: The role of solute/sodium symporters in bacterial signal transduction


Transporters of the solute/sodium symporter (SSS) family transport sugars, amino acids, vitamins, and ions in cells of all domains of life. However, SSS proteins also form domains in prokaryotic signal transduction systems. The physiological significance and molecular mechanism of function of SSS domains in these systems are not known. Given that covalent binding between a transporter and a signal transduction system has emerged during evolution and has become widespread in the domain of bacteria, including Proteobacteria, this project focuses on elucidating the functional significance and underlying molecular mechanisms of the interactions between the SSS domain and signal transduction system. Using the sensor kinase/response regulator system MxtR/ErdR of the soil bacterium Pseudomonas putida KT2440 as a model, we test a possible direct control of signal transduction by the SSS domain of MxtR in response to ion gradients, membrane potential, binding and/or transport of a solute. Furthermore, we investigate the influence of other sensor kinase domains on a possible transport activity of the SSS domain in response to intracellular stimuli. We expect the results of this project to provide new insights into the function of SSS family proteins and a better understanding of the regulatory networks of P. putida KT2440. These findings may facilitate the use of the genetically accessible, solvent-resistant and safe bacterium as a platform for industrial biosynthesis (for example, plastic-like polymers, biosurfactants). Since homologs of the MxtR/ErdR system are also found in important pathogens such as Pseudomonas aeruginosa, we also expect to contribute to better understand the regulatory network of these bacteria.

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

Henriquez, T. and Jung, H. (2021) Involvement of the MxtR/ErdR (CrbS/CrbR) two-component system in acetate metabolism in Pseudomonas putida KT2440. Microorganisms 9, 1558

Henriquez, T., Wirtz, L., Su, D., and Jung, H. (2021) Prokaryotic solute/sodium symporters: versatile functions and mechanisms of a transporter family. Int. J. Mol. Sci. 22, 1880

Wirtz, L., Eder, M., Schipper, K., Rohrer, S., and Jung, H. (2020) Transport and kinase activities of CbrA of Pseudomoinas putida KT2440. Sci. Rep. 10, 5400


Prof. Dr. Kirsten Jung (Microbiology)
Title: The role of mRNA modification in the stress response of bacteria


Methylation of mRNA is an important regulator of physiological processes in eukaryotes, but it has not been thoroughly studied in prokaryotes.
It will be the task of the doctoral researcher to characterize the dynamics of mRNA modifications (m6A and m5C) in bacteria under different stress conditions (acid stress, cold stress and heat stress), identify methylated transcripts, and characterize RNA-protein interactions using biophysical methods. In addition, mutants lacking the methylation sites will be constructed and analyzed for their stress response. Work on this topic requires a combination of biochemical (RNA biochemistry), systemic (e.g., RNA-Seq, Ribo-Seq) and microbiological techniques (e.g., construction of single-point mutants and reporter strains).


The candidate should have an MSc. (or equivalent degree) in Life Sciences (Biochemistry, Chemistry, Biology, Microbiology). The candidate should be highly motivated and determined with a strong interest in biochemistry and the application of interdisciplinary approaches.


Experience in RNA biochemical methods and bioinformatics is required.


LSM and Research Training Group of CRC 1309 ( provide a tailor-made training environment for doctoral researchers active in the field of “Chemical Biology of Epigenetic Modifications".


 Prof. Dr. David Keays (Developmental Neurobiology)
Title: Modelling TUBB2A Associated Disease States with Cerebral Organoids.


This project will provide mechanistic insight into human brain malformations caused by mutations in a beta-tubulin gene, TUBB2A, by exploiting advanced human stem cell-based methods.The human cerebral cortex is one of the most complex biological structures in biology. Its development involves a carefully orchestrated sequence of events that can be divided into three major stages: i) the generation of neurons; ii) the migration of neurons from their place of birth into the developing cerebral cortex; and iii) and the maturation and differentiation of neurons forming functional circuits.

Cortical development is dependent on correctly functioning microtubules: dynamic, scaffold-like polymers composed of alpha- & beta-tubulin heterodimers. Microtubules generate the intracellular forces required for each major stage of cortical development: i) they form the mitotic spindle during cell division, facilitating the separation of sister chromatids; ii) they enable translocation of the nucleus and extension of the leading process during neuronal migration; iii) and microtubules polymers extend and maintain large and longstanding axons in mature neurons that enable connectivity with often distant regions of the brain.
TUBB2A encodes for a beta-tubulin protein. Different TUBB2A variants give rise to a spectrum of cortical brain malformations including microcephaly (reduced brain size) and lissencephaly (smooth or broadly convoluted cortical folds). The specific cellular mechanisms underlying cortical malformations are poorly understood. We hypothesise that TUBB2A mutations affect the correct assembly, stability and/or the dynamics of microtubule polymers which, in turn, perturbs correct neuronal proliferation, migration and/or differentiation during cortical development.

This project will investigate TUBB2A-related disease using human stem cells. We have obtained skin fibroblasts from individuals with cortical malformations harbouring TUBB2A mutations and these have been reprogrammed to induced pluripotent stem cells (iPSCs). We have additionally used CRISPR/Cas9 to ‘repair’ patient mutations back to wild-type sequence, generating suitable control lines to pinpoint the mutation-specific effects on cortical development.

The project will involve differentiation of patient and control iPSCs into 2D neuronal cultures to determine the effects of TUBB2A variants on microtubule biology and function. Furthermore, to characterise potential consequences of TUBB2A mutations on neurogenesis, neuronal migration, and cortical organisation, we will use patient and control iPSCs to generate cerebral organoids, 3D neuronal cultures that recapitulate early stages of human cortical development.

Interested students should contact Professor Keays via e-mail


Prof. Dr. Andreas Klingl (Plant Sciences)
Title: A detailed analysis of the 3D architecture of the plant-microbe interface via TEM and STEM tomography


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).


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

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-
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:
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: Hardening corals against climate change

Climate change causes ocean warming and acidification with dramatic effects, including coral bleaching and impaired coral reef-building. Several approaches have been designed to cope with this problem, including hardening the algal partner of the symbiosis that forms corals. Our concept is to use adaptive laboratory evolution to rapidly evolve the algal symbiont to become more resistant to relevant stresses including high temperature and high light. Reintroduction of the evolved algae in the symbiotic relationship will then be tested for enhanced performance of the coral



Dr. Macarena Marín (Genetics)
Title:Life within a cell


Nitrogen-fixing rhizobia can live endosymbiotically inside specialized cells in the roots of legume plants. No other living cell-type can host rhizobia. Despite the uniqueness of this process and its importance for agriculture, our molecular understanding of the cellular adaptations required to host rhizobia inside root nodule cells remains limited. By comparing the transcriptomes of root nodules that can and cannot host rhizobia, we identified candidate genes that are likely to mediate this process. Among these, genes with functions associated with cell wall plasticity and cell expansion were specifically upregulated in infected nodules. In this project, we will investigate the function of these genes and evaluate if they play a role in hosting endosymbiotic bacteria. To this end we will: i) generate mutants of selected candidates using CRISPR/Cas editing and assess their phenotypes, ii) analyze the spatiotemporal control of promoters driving the expression of candidate genes, and iii) use advanced microscopy and mathematical modelling to understand the relation between cell wall plasticity and cell expansion. The molecular understanding of how plant cells host endosymbiotic bacteria will aid in the long-term goal of transferring endosymbiotic nitrogen-fixation to other plants, which will hopefully reduce the need of using environmentally harmful nitrogen fertilizers.

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



Dr. Arne Weiberg (Genetics of Plant-Pathogen Interaction)
Title: Pathogen extracellular vesicles in RNA effector delivery


The fungal plant pathogen Botrytis cinerea and the oomycete Hyaloperonospora arabidopsidis deliver small RNA effectors into their host plants in order to suppress plant immunity genes (1, 2); a process known as cross-kingdom RNA interference (3). How are pathogen small RNAs transported into plant target cells? Recent studies suggest that extracellular vesicles (EVs), lipid particles that are released by different types of living organisms (4), play an important role in plant cross-kingdom host-pathogen communication (5). Are EVs a means of RNA transportation during plant infection?

We are seeking for a talented young career researcher, who is passionate about molecular biology and RNA science, and is willing to take together with us the next step for uncovering the fascinating, yet unknown mechanisms involved in plant-pathogen cross-kingdom RNAi. Our research project offers to elucidate the molecular mechanisms and functions of EV-based sRNA transport from pathogenic fungi or oomycetes into the host plants Arabidopsis and tomato. By mass spec analysis of Botrytis EV-loaded proteins we identified prime candidates to be characterized for their roles in sRNA transport and cross-kingdom RNA communication. Your task will be to unravel their function by applying modern fungal and plant genetic, biochemical, and cell biological methods that will pave the way for a better understanding of the RNA delivery mechanisms from pathogens into host plants.

1. F. Dunker, …, A. Weiberg, Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. Elife 9, e56096 (2020).
2. A. Weiberg et al., Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways. Science 342, 118-123 (2013).
3. A. Weiberg, M. Wang, M. Bellinger, H. Jin, Small RNAs: a new paradigm in plant-microbe interactions. Annu Rev Phytopathol 52, 495-516 (2014).
4. A. Ruf, …, A. Weiberg, Spotlight on plant RNA-containing extracellular vesicles. Curr Opin Plant Biol 69, 102272 (2022).
5. S. Kwon, C. Tisserant, M. Tulinski, A. Weiberg, M. Feldbrügge, Inside-out: From endosomes to extracellular vesicles in fungal RNA transport. Fung Biol Rev 34, 89-99 (2019).