DAAD-LSM doctoral projects 2021
- You have to apply through our online application tool which is open until 30 November 2020, 12:00 noon CET !
- The offered projects of this DAAD-GSSP application cover most areas of natural and life sciences from Anthropology and Human Biology, Cell and Developmental Biology, Genetics, Ecology, Microbiology, Molecular Biology, Biochemistry, Cell and Developmental Biology, Ecology, Evolutionary Biology, Plant Sciences, Pharmacology, Systematics.
- On the online application tool three projects can be selected.
- Please check our faculty members´research here
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Title: Evolution of gene regulatory networks in primates inferred by perturbations
Background:Understanding how gene regulation evolves is crucial to understand biological diversity and human biology. Comparisons across primates are of particular relevance not only because they inform human-specific evolution but also because they bridge the gap between human and mouse, our most important model organism. While cross-species comparisons of expression levels have been amply conducted, broadening the scope to study gene regulation in genetically accessible and comparable primate cell systems is necessary to fully leverage the unique information encoded in the molecular evolution of primates. With the combination of CRISPR-based perturbations and single-cell transcriptomic read-outs, a game-changing technology to study gene regulation has recently emerged.
Specific aims and technologies: Within this project induced pluripotent stem cells (iPSCs) from different primates will be generated that express an inducible dCas9-KRAB to repress transcription factors in a high-throughput CRISPRi screen with single-cell RNA-seq readout. The project will include reprogramming cells to iPSCs, characterizing iPSCs, cloning, CRISPRi screening and single-cell RNA-sequencing (10x). Good molecular biology and cell culture skills are required and aptitude for quantitative and statistical analyses recommended.
Prof. Dr. Peter Geigenberger (Plant Sciences)
Title: It’s do or die – Interactions between plant signaling and metabolic pathways under hypoxia and reoxygenation
Plants cannot build up an active oxygen transport system. Therefore, plants experience low-oxygen conditions in highly metabolically active and very dense tissues during their development and in response to decreased oxygen availability in the environment during waterlogging or flooding (Geigenberger 2003). When oxygen concentrations drop, a complex network of regulatory signals and transcription factors leads to a tremendous rearrangement of the plant cell metabolism to oxygen-saving pathways, resulting in a dramatic decrease of energy in the cell (Paul et al. 2016). Once the oxygen returns to the hypoxic environment during reoxygenation, it is therefore crucial to reestablish normoxic metabolism and redox balance to prevent cell damage by the formation of harmful reactive oxygen-species. In the present project, the underlying signals and mechanisms regulating and coordinating the acclimation of plants to hypoxic conditions and reoxygenation will be investigated. This will involve a combination of systems biology and hypothesis driven approaches including genetic, biochemical and molecular-physiological methods.
Geigenberger P (2003) Response of plant metabolism to too little oxygen. Current Opinion in Plant Biology 6, 247-256
Paul MV, Iyer S, Amerhauser C, Lehmann M, van Dongen JT, Geigenberger P (2016) Oxygen sensing via the ethylene response transcription factor RAP2.12 affects plant metabolism and performance under both normoxia and hypoxia. Plant Physiology 172, 141-53
Prof. Dr. Nicolas Gompel (Cell/Evolutionary Biology)
Title: The epigenetic origin of a behavioral shift in Drosophila
The invasive pest fly Drosophila suzukii has invaded the world over the last decade. Among possible assets that have facilitated this invasion, D. suzukii displays a remarkable plasticity to seasonal temperature changes. In addition to striking morphological changes in, for instance color, between flies developing at room temperature (summer morphs) and flies developing at low temperature (winter morphs), we have established that these seasonal morphs also differ markedly in their innate behaviors. In particular, the search for a suitable substrate to lay eggs appears to align with the resources available during the respective seasons. Indeed, winter morphs show an innate preference for decaying fruits, while summer morphs with the same genome preferentially lay their eggs in ripe fruits. This clear-cut behavioral shift is, therefore, likely controlled by epigenetic changes affecting the development or the function of the nervous system, or both. This project aims at identifying how seasonal temperature induces epigenetic differences and unravelling their consequences on the neural circuits that govern innate behavioral preferences.
Study system and specific goals:
Drosophila suzukii is established as a model in the Gompel lab and is amenable to molecular genetics and transgenics approaches.
The project will combine single-cell RNA-seq and single-cell ATAC-seq on the brain of seasonal morphs to identify which loci may have different regulatory states. These loci will constitute entry points to analyze the function and connectivity of the neurons that express them. In addition, the project will examine neuronal activity in whole brains and olfactory neurons of winter and summer morphs, using calcium imaging, to identify brain regions that process information differentially.
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.
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 cation channels and lung disease
The most prevalent chronic lung diseases today are lung fibrosis and COPD (chronic obstructive pulmonary disease), the latter one affecting nearly 300 million people worldwide, resulting in the death of 3 million individuals each year. Currently, there are no drugs available that can cure lung fibrosis, emphysema formation or COPD. Hence, there is an urgent need for novel and innovative strategies and targets. In COPD and emphysema patients, the lung is chronically inflamed. In response to cigarette smoke or inhalation of environmental and occupational pollutants such as metals in asbestosis or silicosis, high levels of dust in coal mining and certain gases, cells such as neutrophils, T-lymphocytes, B cells and macrophages accumulate. When activated, these cells initiate an inflammatory cascade that triggers the release of inflammatory mediators such as tumour necrosis factor alpha (TNF-α), interferon gamma (IFN-γ), matrix-metalloproteinases (MMP-6, MMP-9), cathepsins, C-reactive protein (CRP), interleukins (IL-1, IL-6, IL-8) or fibrinogen (Barnes, 2004; Vlahos and Bozinovski, 2014). These inflammatory mediators sustain the inflammatory process and lead to tissue damage as well as a range of systemic effects. In the setting of COPD, respiratory tract infections, both acute and chronic, also occur with increased frequency (Sethi et al., 2010). These infections contribute considerably to the clinical course of COPD patients and constitute a significant comorbidity in COPD.
Endolysosomal cation channels, in particular TRPML channels (TRPML1, TRPML2, TRPML3) and two-pore channels (TPC1, TPC2) have been shown recently to be highly expressed in macrophages (Samie et al., 2010; Cang et al., 2013), but also in alveolar epithelial cells, and have been postulated to control intracellular vesicle trafficking and endolysosomal exocytosis, and to play critical roles in endocytosis and phagocytosis. More here
Prof. Dr. Kirsten Jung (Microbiology)
Title: Communication between host and the human gut microbiota
Bacteria as unicellular organisms are constantly exposed to changing conditions of the external environment. Given the strong selection pressure, it is not surprising that bacteria have developed sophisticated signal transduction systems to sense changing external parameters, such as nutrients, osmolarity, cell density, but also host signals and to adapt structure, physiology and behavior accordingly.
The research of my group focuses on elucidating the molecular mechanisms of stimulus perception and signal transduction. Furthermore, we investigate the complexity of regulatory networks in correlation with phenotypic heterogeneity. Finally, we analyze the function and variability of post-translational modification of elongation factor P (EF-P), a ribosome-binding protein that supports the incorporation of polyproline motifs into proteins.
The aim of the project is to analyze phenotypic changes of different bacterial species of the human microbiome after their exposure to host signals. We will specifically focus on the response of bacteria, such as Pseudomonas aeruginosa, to the stress hormone epinephrine, but also to sex hormones such as estrogen. Intracellular targets of these hormones shall be elucidated in close collaboration with the group of Prof. Dr. Stephan Sieber, Technical University Munich.
The project will be associated with SFB 1371 “Microbiome Signatures”.
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
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
Prof. Dr Hans-Henning Kunz/PD Dr. Serena Schwenkert (Plant Sciences)
Title: Systematic investigating the physiological relevance of outer envelope membrane proteins enabled by the design of a new artificial miRNA library tool
Being home to photosynthesis, the chloroplast is at the heart of plant metabolism. The organelle is optimized for light harvesting and thus represents a major sensing hub to collect information on the plant’s environment. This feature is pivotal for plants to respond to biotic and abiotic stress. Its physiological and sensing capacities make the plastid a highly fascinating subject of research that provides a rich learning experience for graduate students.
Plastids evolved through endosymbiosis between a cyanobacterium and a protist host cell. Reminiscent of this event, the chloroplast is surrounded by two membranes, the inner and outer envelope membrane (OEM). The OEM harbors less than 50 identified proteins. Whatever protein, metabolite, ion or molecular signal is leaving or entering the plastid has to pass through one of the OEM proteins. Exciting work from our lab has shown, that some OEM proteins can be highly selective while others possess broad substrate specificity. For example, we recently identified Jassy, which exports a Jasmonate precursor from the plastid, thus contributing to cold acclimation and pathogen resistance in Arabidopsis.
What is currently missing is a systematic tool that allows to study the protein function with a more system biology approach. This is not straight forward as many OEMs have major implications for plastid and overall plant function. Consequently, OEM gene losses often times are lethal. To overcome this road block, we have calculated 36 artificial micro RNAs and called it the OEMi library. The OEMi library can effectively suppress all 50 OEM proteins to varying degrees. A small proof-of-concept confirmed the feasibly of our approach and already yielded new unexpected phenotypes.
Initially, the fellow will finish the cloning of the library and share the tool with the plant science community though a first publication. Meanwhile, (s)he will transform the library into an established plastid Ca2+ reporter mutant line. The resulting population will be screened for mutants with differences in stromal Ca2+ loading by confocal microscopy, mutants sensitive to cold stress by plant phenotyping, and lastly mutants that show altered photosynthetic responses to light stress. Subsequently, the mutants and the compromised gene(s) will be characterized in detail. Our international group has decades of biochemical expertise that includes a large set of specific OEM antibodies. The project will be closely associated to the collaborative research consortium ‘The green hub’, providing a cutting-edge platform for national and global collaborations with leading experts in the field. Our group represents an ideal and welcoming training environment for a motivated student to pursue this exciting systems biology project focused on revealing the importance of the plastid OEM.
Bölter B, Mitterreiter MJ, Schwenkert S, Finkemeier I, Kunz HH. (2020) The topology of plastid inner envelope potassium cation efflux antiporter KEA1 provides new insights into its regulatory features. Photosynth Res.;145:43-54.
Guan L, Denkert N, Eisa A, Lehmann M, Sjuts I, Weiberg A, Soll J, Meinecke M, Schwenkert S. (2019) JASSY, a chloroplast outer membrane protein required for jasmonate biosynthesis. Proc Natl Acad Sci U S A., 116:10568-10575
Kunz HH, Gierth M, Herdean A, Satoh-Cruz M, Kramer DM, Spetea C, Schroeder JI. (2014) Plastidial transporters KEA1, -2, and -3 are essential for chloroplast osmoregulation, integrity, and pH regulation in Arabidopsis. Proc Natl Acad Sci U S A. 111:7480-5.
Prof. Dr. Dario Leister (Plant Sciences)
Title: Enhancing photosynthesis by synthetic biology and adaptive laboratory evolution
In this project, parts of the light reactions of photosynthesis from very different species will be combined in the cyanobacterium Synechocystis 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 stress. Corresponding mutations will be identified by whole-genome sequencing and tested for their potential to enhance stress tolerance in Synechocystis and other species.
Prof. Dr. Richard Merrill (Evolutionary Biology)
Title: Evolution and genetics of visual mate preferences in tropical butterflies
Many closely related animal taxa remain separate not because their individuals fail to produce viable offspring, but because they effectively ‘choose’ not to do so in the first place. However, although the significance of behavioural barriers for speciation has been recognized since the Modern Synthesis, we know little of the genetics of changes in mating preferences, or variation in behaviours across natural populations more broadly.
The Neotropical Heliconius butterflies are well known for their bright warning patterns, which also act as mating cues. Using a combination of behavioural QTL and gene expression analyses, we have recently identified a handful of candidate genes underlying differences in visual preference behaviours in the closely related species Heliconius cydno and H. melpomene. Building on our previous results, this project will explore the evolution of this behavioural locus across the cydno-melpomene clade more broadly, both during development and across evolutionary time. In particular, the project will exploit the potential for adaptive introgression of behavioural alleles across the species boundary to better understand the genetic and developmental basis of visual preferences. The project will likely combine extensive behavioural experiments and field work in the tropics with modern molecular and genomic techniques. Within the framework of our research on behavioural genetics in Heliconius, the student will be encouraged to follow his/her own interests.
Prof. Dr. Stylianos Michalakis (Gene Therapy)
Title: Novel gene therapy approaches for inherited eye diseases
Scientific background. The group works on the development of recombinant adeno-associated virus (AAV) vector-based gene therapies for eye diseases. Vectors developed by the group have been already translated into clinics within the RD-CURE consortium (http://www.rd-cure.de) that successfully completed the first ocular gene therapy trial on CNGA3-linked achromatopsia (https://www.clinicaltrials.gov/ct2/show/NCT02610582) and also initiated the first PDE6A-linked retinitis pigmentosa gene therapy trial. While these projects confirm the translational potential of AAV-based gene therapy vectors, there are still aspects that need further improvement. The group is working on improvement of several vector technologies, but also on expanding the treatment options to other retinal disorders inherited, but also more common disorders with no clear genetic link.
Specific aims and methodology. The goal of this project is to development novel optimized retinal gene therapies based on next generation AAV vector technologies. Gene-specific and/or gene independent treatment approaches will be designed and evaluated in vitro. The novel gene therapy approaches will be further optimized for efficacy in relevant mouse models of inherited blinding diseases. The methodology will include state-of-the-art in vitro and in vivo biochemical, genetic, cell biological and viral gene transfer methods. Potential candidates should have a strong interest and background in mouse physiology and anatomy (focus on the eye), cell biology, molecular biology, gene therapy (virology), and imaging. Particular interest and experience in bioinformatics, (big) data processing (e.g. RNAseq, proteomics, imaging data) is welcome.
Further information and selected literature.
Böhm S*, Splith V*, Riedmayr LM, et al. (2020) A gene therapy for inherited blindness using dCas9-VPR-mediated transcriptional activation. Sci Adv 6(34): eaba5614.
Fischer MD*, Michalakis S*, Wilhelm B, et al. (2020) Safety and Vision Outcomes of Subretinal Gene Therapy Targeting Cone Photoreceptors in Achromatopsia: A Nonrandomized Controlled Trial. JAMA Ophthalmol 138(6):1-9.
Petersen-Jones SM, Occelli LM, Winkler PA, et al. (2018) Patients and animal models of CNGbeta1-deficient retinitis pigmentosa support gene augmentation approach. J Clin Invest 128(1): 190-206.
Dr. Tamara Mikeladze-Dvali (Cell Biology)
Title: Studying the oral-facial-digital (ODF) syndrome proteins in C. elegans
Centrioles fulfill many import functions for the development of an organism. In mitotic cell centrioles assemble the peri-centriolar material and act as the main microtubule organizing centers of animal cells (Figure 1). In differentiated cells centrioles, also called basal bodies, doc at the membrane and serve as templates for cilia elongation (Figure 2). Therefore, abnormalities in centriole formation and function are implicated in a in broad spectrum of human diseases ranging from cancer to congenital heart diseases. Among these conditions is the oral-facial-digital (ODF) syndrome, which is associated with microcephaly, mental retardation and malformations of the face and digits. Several mutations in the gene coding for the centriolar protein C2CD3 are tightly linked to the ODFXIVsyndrome. The functional homologue of C2CD3 in C. elegans is protein called Spindle-ASsembly abnormal-1. Loss of the Spindle-ASsembly-abnormal-1 function leads to the destabilization of the centriolar structure and monopolar spindle formation during mitosis (von Tobel et al. 2014). Animals carrying this a mutation lead are usually lethal.
The aim of this project is to establish an ODF-syndrome model in C. elegans. In order to uncover molecular mechanisms leading to the different aspects of the ODF-syndrome, we plan to identify disease-related, critical regions and homologous mutations in C. elegans. Using genome editing tools these mutations will be introduced in Spindle ASsemblyabnormal- 1 and the implications studied in the context of C. elegans development, specifically during neurogenesis and spermatogenesis.
1. von Tobel L, Mikeladze-Dvali T, Delattre M, Balestra FR, Blanchoud S, Finger S, et al. SAS-1 Is a C2 Domain Protein Critical for Centriole Integrity in C. elegans. PLoS Genet
10(11): e1004777 (2014). https://doi.org/10.1371/journal.pgen.1004777
2. Thauvin-Robinet, C., Lee, J., Lopez, E. et al. The oral-facial-digital syndrome gene C2CD3 encodes a positive regulator of centriole elongation. Nat Genet 46, 905–911
3. Franco, B., Thauvin-Robinet, C. Update on oral-facial-digital syndromes (OFDS). Cilia 5, 12 (2016). https://doi.org/10.1186/s13630-016-0034-4
PD Dr. Dejana Mokranjac (Cell Biology/Bichemistry)
Title: Molecular mechanisms of biogenesis and quality control of mitochondria
Mitochondria are fascinating cell organelles that not only produce most of ATP our cells need but are also key to initiating apoptosis. Though mitochondria contain their own genome, the vast majority of mitochondrial proteins are encoded in the nuclear genome. Thus, the proper structure and function of mitochondria critically depend on import of over 1000 different proteins that are synthesized on cytosolic ribosomes as precursor proteins and need to be transported to the correct mitochondrial subcompartment in order to reach the final place where they fulfil their biological function. About 70% of mitochondrial proteins use an N-terminal presequence as a mitochondrial targeting signal and are translocated with the help of the TOM and TIM23 complexes in the outer and inner mitochondrial membranes, respectively. The presequence pathway is used by essentially all matrix proteins, a large number of inner membrane proteins and even some intermembrane space- and outer membrane proteins. Translocation of proteins along the presequence pathway requires two energy sources – the membrane potential across the inner membrane and ATP in the matrix. The TOM and TIM23 complexes are highly complex molecular machines that consist of ca. 20 highly evolutionary conserved proteins, the majority of which are essential for cell viability. Translocation of proteins along the presequence pathway is not only essential for biogenesis of mitochondria but is also used by the cells to monitor the quality of their mitochondria. We are fascinated by the versatility of this pathway and the rich biochemistry behind it. By combining biochemistry, cell biology and yeast genetics, we aim to obtain a mechanistic understanding of the processes that enable recognition and translocation of proteins along the presequence pathway.
The project will aim to reveal the molecular mechanisms of how the TIM23 complex converts the energy of ATP hydrolysis into unidirectional transport of proteins into mitochondria and how this process is used by the cells to monitor the quality of their mitochondria.
To join us, you should have fun in doing basic research and preferably have previous experience in protein biochemistry and/or yeast genetics.
Prof. Dr. Martin Parniske
Title: Harnessing natural genetic resources to defend fruits against insect attack
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 the long term we aim to identify the genes and mechanisms underlying this resistance and thus provide alternative strategies that can replace insecticide application for the production of healthy fruits.
Prof. Dr. John Parsch (Evolutionary Biology)
Title: Chromosome-specific gene regulation in Drosophila
Species with heteromorphic sex chromosomes, such as the X and Y
chromosomes found in mammals and Drosophila, have evolved special
mechanisms to regulate the expression of sex-linked genes. In the soma
of Drosophila males, the expression of genes on the X chromosome is
up-regulated approximately two-fold to compensate for its monosomy. In
contrast, in the Drosophila male germline the expression of X-linked
genes is suppressed. The molecular genetic mechanism for this
suppression is poorly understood. In this project, we will study the
genes involved in X suppression and determine their molecular functions.
This will be done using mutant flies deficient in this process. The
goals are to identify the specific genes responsible for X suppression,
elucidate their role in gene regulation and their potential interactions
with genes known to be involved in somatic X chromosome dosage
Prof. Dr. Silke Robatzek (Genetics, Plant Health)
Title: Understanding the genetic basis of immunity against the multi-host pathogen Xylella
Emerging and re-emerging disease epidemics represent ongoing challenges to cultivation of crop plants. One of the recent disease epidemics is caused by Xylella fastidiosa, a generalist bacterium that infects a broad range of hosts, now spreading in Europe and threatening olive production. This project will identify genes that determine the infection outcome of X. fastidiosa in olive by exploring cultivar genetic diversity. We will perform transcriptome profiling of several susceptible and resistant olive cultivars to determine genetic differences associated with infection depending on cultivars. Our bioinformatics analysis will include differential comparative co-expression analysis using WGCNA targeting clusters of co-expressed genes. We will use our RNA-seq data for gene assembly with the opportunity to search for single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) to get a deeper understanding of cultivar diversity as a whole. We will utilize the genetic model host A. thaliana to functionally evaluate the role of selected genes by transgenic expression, and mutants of orthologous genes found by phylogenomic analysis. Our goal is to answer what enables immunity in resistant olives and why immunity fails in susceptible cultivars.
Dr. Arne Weiberg (Genetics)
Title: Molecular function of oomycete non-RxLR effectors in plant host infection
Oomycetes comprise notorious plant pathogens severely reducing global crop yield and causing enormous economic loss. The oomycete H. arabidopsidis represents one of the most used model pathogens to investigate A. thaliana innate immune response to obligate biotrophs. Little is known about the pathogenicity of obligate biotrophs, because they are impossible to grow in axenic culture, thus genetic transformation of these organisms is not achievable.
We have recently developed host-induced gene silencing (HIGS) in A. thaliana for targeted knockdown of genes in H. arabidopsidis. Hereby, we discovered that the H. arabidopsidis non-RxLR, cysteine-rich effector (HaCR)1 is important for host infection by supressing induced plant cell death. We offer a doctoral project to scrutinize the plant molecular targets of HaCR1 by biochemical, molecular genetics and cell biological approaches. In a second project, we propose to apply the HIGS method to identify novel H. arabidopsidis effectors and pathogenicity factors.