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DAAD-LSM doctoral projects 2021

Please note:

  • You have to apply through our online application tool which is open until 30 November 2021, 12:00 noon CET !
  • 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.
  • Please check our faculty members´research here
Research groups
 in collaboration with Natascha Turetzek and Viktor Baranov
in collaboration with Prof. Frank Grutzner, University of Adelaide
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.

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: Endolysosomal TRPML and two-pore channels in neurodegenerative disease

Endolysosomal TRPML channels and TPCs are gaining more and more attention as important regulators of many different functions in a diverse set of cells including immune cells, cancer cells, cells of the central nervous system, melanocytes and pigmentation, parietal cells in the stomach, hepatocytes, cardiomyocytes and many more. Previously established or postulated functional roles of these ion channels in the endolysosomal system include trafficking, fusion/fission, exocytosis, endocytosis, autophagy, and pH regulation, and in several studies TRPMLs and TPCs have been found to play direct roles in virus (e.g. Ebola) and bacterial toxin trafficking, or bacteria exocytosis (demonstrated mainly for TPCs and TRPML2/3), in the modulation of secretory lysosomes, granzyme B content and tuning of effector function in NK cells (TRPML1), in dendritic cell (DC) migration and DC chemotaxis (TRPML1), or in chemokine release from LPS-stimulated macrophages (TRPML2), in hepatocytes (cholesterol accumulation, TPC2), in melanocytes as regulators of pigmentation (TPC2), in different cancer cells (TRPML1 and TPCs, e.g. in migration, invasion, proliferation), and in the development of lysosomal storage diseases (mutations of TRPML1 cause mucolipidosis type IV in children and TRPML1 modulation has an effect also on NPC1 or Charcot-Marie Tooth disease type 4J (FIG4)). Both, TRPMLs and TPCs reside in different locations in the endolysosomal system (TRPML1 and TPC2 mainly in late endosomes and lysosomes), others also in early endosomes and recycling endosomes. TRPMLs and TPCs are both non-selective cation channels permeable for calcium and sodium and they are both activated by PI(3,5)P2, while TPCs are also activated by NAADP, most likely indirectly through a recently discovered interaction partner, JPT2.
We have recently found evidence for an important novel role of one of the two-pore channels in neurons and neurodegenerative diseases (Krogsaeter et al. MS in prep.). In this study we made use of a new GFP reporter mouse model for this channel, the endolysosomal patch clamp technology, and a multitude of molecular and cell biology techniques to corroborate our data and findings. Furthermore, we established iPSC models for several neurodegenerative lysosomal storage disorders used as human disease models (in combination with CRISPR/Cas9). The incoming PhD student will help support to further investigate these phenotypes on a molecular and cellular level and he/she will generate new iPSC models for other relevant diseases, supported by a Postdoc and other staff in the lab. The student will learn a plethora of techniques involving also in-vivo work.

Prof. Dr. Joachim Haug (Evolutionary Developmental Palaeobiology)
Title: Repeated loss and gain of the blood feeding mouth parts in non-biting midges
Collaborative Project: Natascha Turetzek (Zhang), Viktor Baranov and Joachim Haug

Blood-feeding of flies (Diptera) is one of the longest-enduring and most important types of insect-vertebrate interaction. Existing potentially for over 200 million years, blood-feeding of flies has shaped numerous facets of the evolution of different lineages of Vertebrate and the behavior of their representatives – from frogs hiding from eavesdropping frog-biting midges (Corethrellidae) to the economic development of the countries being slowed down by the spread of malaria by mosquitos.
Therefore, understanding the evolution of blood feeding is of profound interest. One extremely remarkable aspect of the evolution blood-feeding in flies is a rampant loss and re-gaining of functional mouthparts in “non-biting” midges (Diptera, Chironomidae). All extant non-biting midges, except for two species poor groups, are, as they name suggest, not only not biting anyone, but do not feed as adults at all. Nevertheless, the growing fossil record of this group shows that the two relic groups still possessing functional mandibles may appear unusual today but represented the norm in the past. In the course of 210 million years non-biting midges lost and regained the use of mandibles at least four times. This represents an interesting case of losing a complex and important character, yet apparently retaining a regulatory apparatus required for re-acquiring it. Comparative developmental studies on the evolutionary diversification of euarthropod appendages are prime examples to understand the genetic basis responsible for evolutionary changes. The recruitment of newly evolved genes after gene duplications, gene regulatory network changes as well as co-option of existing networks were found to play a crucial role for several morphological innovations. However, most studies focus on subtle appendage modifications or an entire loss. Revealing the genetic basis of the repeated gain and loss of the biting mandible in non-biting midges will give further insights on the evolution of innovative traits.
By using cutting edge developmental and bioinformatic methods, such as RNA sequencing, de novo transcriptome assembly, Differential gene expression calling, fluorescent in-situ hybridization combined with functional studies like RNA interference and CRISPR as well as examining a growing set of fossil finds will allow the prospective student to disentangle this complex riddle, using molecular, developmental, bioinformatic, phylogenetic and paleontological methods.

plate 25762_2-1

Figure 1. A. Mandibulate female of “non-biting” midge female from 38 million years old Ukrainian amber (confocal scanning laser microscopy); B. Mandibulate female of “non-biting” midge from 50 million years old Indian amber, µCT-synchrotron tomography.

Prof. Dr. Kirsten Jung (Microbiology)
Title: Translational Regulation as Strategy to Survive under Acid Stress in Escherichia coli

On Earth, there are many habitats that have a 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. However, under strong acid stress, the intracellular pH of neutralophilic bacteria decreases by approximately one pH unit, which has a considerable impact on the protonation states of all biological molecules, and can affect their charge, structure and function. In our preliminary work, we exposed Escherichia coli to different degrees of acid stress, and measured the changes in the rates of synthesis of all proteins by using RiboSeq. It will be the aim of the project to identify and characterize proteins that undergo translational regulation under strong acid stress. In addition, their contribution to acid stress survival will be studied.

Ude S, Lassak J, Starosta AL, Kraxenberger T, Wilson DN, Jung K (2013) Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches. Science 339: 82–85

Prof. Dr. Andreas Klingl (Plant Sciences)
Title: A comparative approach to the 3-dimensional structure of the plant-microbe interface using advanced electron microscopy


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: Molecular mechanisms controlling cell infection in endosymbioses

Legume plants host nitrogen-fixing rhizobia inside root nodule cells. Intracellular accommodation is critical for the effectiveness of root nodule symbiosis, as it is in this intracellular stage when rhizobia differentiate into nitrogen-fixing bacteroids. Our molecular understanding of the tissue and cellular adaptations required to host rhizobia inside nodules remains extremely limited. Using a comparative transcriptomic approach, we identified 167 differentially regulated genes between infected and non-infected nodules. Among these, genes with functions associated with cytoskeleton, cell wall modifications, and cell expansion were specifically upregulated in infected nodules. In this project, we will use these candidates to investigate the genetic basis of cell infection by i) generating mutants in specific candidates using CRISPR/Cas technology and assessing their phenotypes, ii) using advanced microscopy and mathematical modelling to understand the relation between cell infection and cell expansion, iii) analyzing the spatiotemporal control of promoter activity driving the expression of infection and expansion reporters, and iv) identifying interactors. The molecular understanding of how plant cells can host endosymbiotic rhizobia will aid the long term aim to transfer this endosymbiosis to other organisms.


Dr. Bart Nieuwenhuis (Evolutionary Biology)
Title: Evolution of sexual asymmetries

Sexual asymmetries, from sexes, to self-incompatibility systems and mating types are commonplace in most eukaryotic taxa. This phenomenon is remarkable when one considers that in a population of two sexes the chance of meeting a compatible partner is reduced by half, compared to a population with universal compatibility. Nevertheless, sexual asymmetries have evolved many times over, suggesting benefits beyond population level compatibility. Two main hypotheses about the origins of asymmetries are that these can i) increase efficiency for mate finding and ii) facilitate the developmental transition between haploid and diploid phases of the life cycle. Mate finding generally occurs by external communication which requires distinguishing self from non-self and autocrine response will reduce efficiency of this distinction thus selecting for differences between
individuals. The developmental switch hypothesis states that conjugation of gametes that differ genetically make the haploid-diploid transition easy to tracked because interactions between unique proteins are only possible at the diploid level, indicating conjugation has occurred. For both hypotheses experimental support is mostly lacking.

The aim of this project is to experimentally test these two hypotheses using the fission yeast *Schizosaccharomyces pombe* as an experimental system. We have generated yeast strains that lack asymmetries, either at the pheromone-receptor level involved in mate finding, or at the mating-type level involved in the switch between haploid and diploid life phases. We will analyze under which circumstances asymmetries are beneficial, performing fitness assays of strains where increasing levels of asymmetries have been reintroduced. Additionally, you will perform experimental evolution with initially symmetrical strains followed by re-sequencing and phenotypic analyses to test the effects of novel mutations on fitness and life-history traits.


Prof. Dr. Christof Osman (Cell & Developmental Biology)
Title: The molecular mechanisms of the quality control of the mitochondrial genome

Mitochondria play a crucial role in energy supply of eukaryotic cells through a process known as oxidative phosphorylation. To fulfill this task, mitochondria depend on their own genome, the mitochondrial DNA (mtDNA), which encodes key subunits of the complexes responsible for oxidative phosphorylation. In contrast to the nuclear genome, mtDNA exist in multiple copies within a cell and these copies are distributed throughout a tubular and reticulated mitochondrial network. Given the importance of energy supply for cellular function, it is not surprising to find that mutations in mtDNA have dire consequences that can cause a multitude of diseases. It is therefore of outstanding interest to elucidate how cells maintain the integrity of mtDNA over generations.

Using yeast as a model organism, we have established a variety of assays to monitor mtDNA quality control and have found that yeast cells intracellularly discriminate between intact and mutant mtDNA and selectively promote generation of cells containing a healthy mtDNA pool. The mechanistic underpinnings of this process, however, remain largely unknown. The goal of this project is to identify the molecular players that facilitate mtDNA quality control and to elucidate their mode of action. The project will entail a wide spectrum of techniques that will include yeast genetics, fluorescent microscopy and protein biochemistry.

As a candidate you should be passionate about cell biology, interested in basic research and have experience in yeast genetics, protein biochemistry and/or microscopy.


Dr. Arne Weiberg (Genetics)
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 et al., Oomycete small RNAs bind to the plant RNA-induced silencing complex for virulence. Elife 9, (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. E. Bielska et al., Highlights of the mini-symposium on extracellular vesicles in inter-organismal communication, held in Munich, Germany, August 2018. J Extracell Vesicles 8, 1590116 (2019).
5. S. Kwon, C. Tisserant, M. Tulinski, A. Weiberg, M. Feldbrügge, Inside-out: From endosomes to extracellular vesicles in fungal RNA transport. Preprints, 10.20944/preprints201911.200213.v201911 (2019).

Prof. Dr. David Keays (Developmental Neurobiology)
Title: The Molecular Basis of Electroreception in Monotremes

Background: The Platypus and Echidna are extraordinary mammals, with unique sensory and morphological features. This includes the ability to detect small electric fields, which is believed to aid the location of their prey. Unlike electroreceptive sharks and teleosts, current evidence suggests that monotremes detect electric fields by relying on trigeminally mediate mucosal receptors which are enriched at the rostral end of the echidna snout, and on the bill of the platypus (See Figure 1A-B). Behavioural and physiological evidence has shown that these receptors are activated by cathodal stimuli in the range of 300 microV to 50mV/cm.

keays project1

Figure 1: (A) Location of putative electroreceptors in the Platypus, long-billed echidna, and short billed echidna (taken from Pedigrew, JEB, 1999.). (B) Diagram showing the morphology of trigeminally innervated electrosensitive mucosal receptors in monotremes (taken from Baker, Springer, 2019).

Proposed experiments: The molecules that enable the detection of electric fields in monotremes are unknown. The utility of a transcriptomic tools to identify putative electroreceptors has recently been demonstrated by Julius and colleagues who showed that the L-type calcium channel CaV1.3 mediates electroreception in Sharks and Skates (Bellono et al, Nature 2017 and 2018). This project will exploit mRNA sequencing of fresh and fixed tissue available through the Monotreme Resource Center (established by Prof. Grutzner) to identify candidate electroreceptors in monotremes. This will be complemented by histological analysis and advanced microscopy techniques to map the anatomical and cellular localisation of these molecules. In addition we anticipate the use of physiological methods, which will be employed to characterise the gating properties of ion channels identified by mRNA sequencing.

The ideal candidate: This ambitious project requires a candidate who has a passion for cellular and molecular neuroscience, is patient, is impervious to scientific failure and who is prepared to spend time in Adelaide, Australia and in Munich, Germany. He/she will ideally have existing experience in molecular biology and/or physiology and demonstrated a capacity for scientific excellence. Applications are open to all nationalities.

Website: and

in collaboration with Prof. Frank Grutzner, University of Adelaide.