DAAD-LSM doctoral projects 2017
- You have to apply with our online application tool.
- The offered projects of this 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, Chemical Biology, Cell and Developmental Biology, Ecology, Evolutionary Biology, Genetics, Microbiology, Plant Sciences, Pharmacology, Systematics, Mycology and Zoology.
- On the online application tool two projects can be selected by indicating a first and a second priority.
- Below please click on the name of the supervisor to get redirected automatically to further information on the research group and the scientific contents.
- For frequently asked questions page provided by the DAAD, please click here or consult their website here for up to date information.
Supervisor: PD Dr. Bettina Bölter (Plant Sciences)
Acclimation in chloroplast protein import
Short term acclimation of chloroplasts to various environmental triggers requires drastic changes in their proteome composition. For example, the amount of photosynthetic complexes needs to be adapted in response to varying light intensities or temperature to ensure optimal performance. Since the majority of chloroplast proteins is encoded in the nucleus and translated as preproteins in the cytosol, posttranslational targeting is a first crucial step towards providing these organelles with the required proteins. To enter the chloroplast, preproteins have to cross the double envelope membrane, which is facilitated by two complex translocation machineries responsible for preprotein recognition and transport. The import process itself is highly regulated at different levels from the outside as well as the inside of the organelle where distinct signalling cascades lead to dynamic acclimation of import activity.
In the proposed project we want to address the following questions:
I. How is thiol and redox mediated import acclimation integrated into cell signalling?
II. Which novel components participate in modulating the transport processes?
To this end, we will combine classical biochemistry and cell biology methods with novel genetic approaches.
Bölter B, Soll J, Schwenkert S. Redox meets protein trafficking. Biochim Biophys Acta (2015) 1847(9):949-56. doi: 10.1016/j.bbabio.2015.01.010
Supervisor: Prof. Dr. Angelika Böttger (Cell Biology)
Title: Developmental signalling pathways and stem cell behaviour in the cnidarian Hydra vulgaris
Little is known about molecular mechanisms that govern stem cell proliferation and differentiation in multi-cellular animals outside the bilaterian clade. This also concerns mechanisms of tumor formation and the key question in tumor biology about the role of cancer stem cells for the initiation, maintenance and growth of tumors. Important signalling pathways involved in stem cell homeostasis have already been found in basal metazoans including Hydra, which have an evolutionary origin that is older than that of bilaterians. Therefore, one might expect to find tumors in these very simple metazoans. A phylostratigraphic approach (see link 1) has predicted that the origin of cancer lies in pre-bilaterian metazoans.
The Notch- and Wnt.-pathways belong to the most important developmental signalling pathways in animals. Canonical Wnt signalling is conserved in Hydra (see link 2). The existence of a Notch homologue, two putative Notch-ligands, the target gene Hes, Su(H) and the co-repressor groucho are also known. Further studies have shown that inhibition of the Notch-pathway in different ways leads to hyperplasia of certain cell-types in the interstitial stem cell lineage (see link 3, 4, 5). However, in these studies the pharmacological inhibitors could only be applied for short periods of time. We suggest that a permanent impairment of the Notch pathway may lead to the formation of tumor-like abnormalities. In addition, the effects of Wnt-signalling on stem cells in Hydra are completely unknown to date, but they are predicted to play a role assuming that the pathway is functionally conserved between higher animals and cnidarians.
With the suggested project we aim to induce neoplasia in the interstitial stem cell lineage of Hydra vulgaris by impairing the Notch and the Wnt-signalling pathways. Therefore, we will express and inhibit Notch and Wnt in certain cell types and at certain differentiation stages. Inducing hyperplasia in one of the conditions will give us insight into the exact cell type and differentiation stage in and at which impairment of these pathways leads to abnormal accumulations. This research will enable us to study the involvement of Notch and Wnt in the regulation of proliferation, apoptosis and differentiation of interstitial stem cells. Finally, inducing stable tumor-like abnormalities will give us the opportunity to study tumor-formation not only in its most simple form but also in a basal animal with an evolutionary origin of 1300 million years, perhaps providing us with insights about the origin of cancer.
- Link: http://www.nature.com/ncomms/2014/140624/ncomms5222/full/ncomms5222.html
- Link: http://www.nature.com/nature/journal/v407/n6801/full/407186a0.html
- Link: http://www.sciencedirect.com/science/article/pii/S0012160613004478
- Link: http://www.sciencedirect.com/science/article/pii/S0012160613004478
- Link: http://www.sciencedirect.com/science/article/pii/S0012160606013777
Domazet-Lošo T., Klimovich A., Anokhin B., Anton-Erxleben F. A., Hamm M. J., Lange C., Bosch T. C. G., Naturally occuring tumours in the basal metazoan Hydra, Nature Communications, (2014), DOI:10.1038/ncomms5222
Käsbauer T., Towb P., Alexandrova O., David C. N., Dall’Armi E., Staudigl A., Stiening B., Böttger A., The Notch signalling pathway in the cnidarian Hydra, Developmental Biologie, (2007), 303:376-390
Münder, S., Tischer, S., Grundhuber, M., Buchels, N., Bruckmeier, N., Eckert, S., Seefeldt, C.A., Prexl, A., Kasbauer, T., Böttger, A., (2013). Notch-signalling is required for head regeneration and tentacle patterning in Hydra. Developmental Biology, 383 (1): 146-57
Münder, S., Käsbauer,T., Prexl, A., Aufschnaiter, R., Zhang, X., Towb, P. and Böttger, A. (2010). Notch signalling defines critical boundary during budding in Hydra, Developmental Biology, 344(1):331-45
Tina Käsbauer, Par Towb, Olga Alexandrova, Charles N. David, Ekaterina Dall’Armi, Andrea Staudigl, Beate Stiening, and Angelika Böttger (2007): The Notch signalling pathway in the cnidarian Hydra, Developmental Biology 303(1):376-90
Supervisor: Prof. Dr. Michael Boshart (Genetics, Biochemistry and Cell Biology)
Title: Signaling mechanisms in parasitic pathogens
Important parasitic pathogens like Trypanosoma and Leishmania belong to phylogenetically distant eukaryotic groups characterized by many unconventional genetic and biochemical features. The group investigates the highly divergent signaling by small second messengers like cAMP, using gene targeting and reverse genetics, proteomics and structure analysis and biochemistry of protein kinases and other signaling proteins. We gain insight into the early evolution of signaling and its role in the biology of the parasite. Highly unusual pathways are promising targets for parasite-specific drug development.
Gould MK, Bachmaier S, et al. (2013) Antimicrob Agents Chemother 57: 4882-4893
Salmon D, Vanwalleghem G, et al. (2012) Science 337: 463-466
Salmon D, Bachmaier S, et al. (2012) Mol Microbiol 84: 225-242
Supervisor: Prof. Dr. Marc Bramkamp ( Microbiology)
Title: Cytokinesis in bacteria: Understanding the molecular mechanisms of division site selection
Bacteria display a high degree of spatial and temporal organization, ensuring reliable generation of offspring and optimized adaption to varying environmental conditions. During the bacterial cell cycle cell division and chromosome segregation are highly coordinated to ensure that division occurs only once per cell cycle and that the genetic material is evenly distributed to the daughter cells. Therefore, correct placement of the cytokinetic machinery is of vital importance and subject to sophisticated regulation. We study division site selection in the Gram positive model organism Bacillus subtilis. We focus on the function and dynamics of the Min (miniature cell) system that is thought to play a major role in restricting assembly of the cell division machinery precisely at midcell. However, the underlying molecular mechanisms driving Min protein dynamics are not understood, yet. Using an interdisciplinary approach including molecular genetics, biochemistry and super-resolution microscopy we address the function of Min proteins in B. subtilis, aiming at a molecular understanding of this fundamental aspect of bacterial cell biology.
Bramkamp, M., Emmins, R., Weston, L., Donovan, C., Daniel, RA., and Errington, J. (2008). A novel component of the division site selection system of Bacillus subtilis and a new mode of action for the division inhibitor MinCD. Mol. Microbiol. 70, 1556-1569
Bramkamp, M. and van Baarle, S. (2009). Division site selection in rod-shaped bacteria. Curr. Opin. Microbiol., 12, 683-688
van Baarle, S. and Bramkamp, M. (2010). The MinCDJ system in Bacillus subtilis prevents minicell formation by promoting divisome disassembly. PLoS One, 5, e9850
Bach JN, Albrecht N, Bramkamp M. (2014) Imaging DivIVA dynamics using photo-convertible and activatable fluorophores in Bacillus subtilis. Front Microbiol. 5:59. doi: 10.3389/fmicb.2014.00059
Supervisor: Prof. Dr. Wolfgang Enard (Primate Genomics, Evolutionary Biology, Computational biology)
Title: Deciphering genetic networks involved in speech and language evolution
Since humans split from their ancestors shared with chimpanzees six million years ago, some genetic changes must have occurred that provide the basis for the human capacity to speak and use language. Two amino acid changes in the transcription factor FOXP2 are currently the strongest candidates for playing a role in this process. Mice that carry these two changes in their endogenous Foxp2 gene show alterations in exploratory behavior, dopamine levels, striatal neuronal morphology and striatal synaptic plasticity suggesting that these changes might have contributed to tuning cortico-basal ganglia circuits for vocal learning during human evolution [1-4].
However, the regulatory networks involved in these changes are not known and it is also not known whether additional changes in these networks might have played a role during human brain evolution. In this project the candidate will use publicly available data and generate own data (RNA-Seq, ChIP-Seq) in developing and adult cortico-basal ganglia circuits to derive candidate genes of the Foxp2 network. These data will be augmented by comparative analyses using species with and without the capacity of vocal learning (c.f. ) to finally test the activity of genes or regulatory elements in functional assays .
During the project the candidate will acquire skills in generating different NGS libraries from mouse brains, in handling large public data sets (e.g. ENCODE, Epigenetic Roadmap), in statistically analyzing RNA-Seq and ChiP-Seq data and in comparing genomic data from different species in order to better understand the evolution of human and mammalian brains.
1. Schreiweis, C., …Enard*, W. and Graybiel*, A. (2014). Humanized Foxp2 accelerates learning by enhancing transitions from declarative to procedural performance. Proc Natl Acad Sci U S A 111, 14253-14258.
2. Enard, W. (2011). FOXP2 and the role of cortico-basal ganglia circuits in speech and language evolution. Current opinion in neurobiology 21, 415-424.
3. Enard, W., et al. (2009). A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell 137, 961-971.
4. Enard, W., Przeworski, M., Fisher, S.E., Lai, C.S., Wiebe, V., Kitano, T., Monaco, A.P., and Paabo, S. (2002). Molecular evolution of FOXP2, a gene involved in speech and language. Nature 418, 869-872.
5. Pfenning, A.R., et al. (2014). Convergent transcriptional specializations in the brains of humans and song-learning birds. Science 346, 1256846.
6. Enard, W. (2014). Mouse models of human evolution. Curr Opin Genet Dev 29C, 75-80.
Supervisor: Prof. Dr. Nicolas Gompel (Evolutionary Ecology)
Title: The role of DNA shape in transcriptional regulation
cis-regulatory elements control where, when, and how much genes are expressed, in response to the binding of transcription factors at specific DNA sites. They play a central role in defining cell identity, organizing cell and tissue interactions during embryonic development, or adapting the physiological response of an organism to changing environment. They are the nodes holding together the myriad of gene regulatory networks that rule the life of a cell. Yet, their mode of action and the determinants of their activity remain very poorly understood.
The present project aims at understanding the clockwork mechanism of a well-defined regulatory element controlling the expression of a pigmentation gene on the wing of Drosophila. The dissection of this element will rely on the use of reporter constructs, biochemistry, and bioinformatics. Two dimensions of the DNA sequence will particularly be scrutinized during the project: the chemical information given by the primary DNA sequence, as well as the structural information given by the local variation in DNA shape. These two properties of the double helix are largely independent, and the role of DNA shape in gene expression has been overlooked.
Abe, N. et al. Deconvolving the Recognition of DNA Shape from Sequence. Cell 161, 307–318 (2015).
Arnoult, L. et al. Emergence and diversification of fly pigmentation through evolution of a gene regulatory module. Science 339, 1423-1426 (2013).
Gompel, N., Prud'homme, B., Wittkopp, P. J., Kassner, V. A. & Carroll, S. B. Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433, 481-487 (2005).
Levine, M., Cattoglio, C. & Tjian, R. Looping back to leap forward: transcription enters a new era. Cell 157, 13-25 (2014)
Prud'homme, B. et al. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440, 1050-1053 (2006).
Rohs, R., West, S. M., Liu, P. & Honig, B. Nuance in the double-helix and its role in protein-DNA recognition. Current opinion in structural biology 19, 171-177 (2009)
Zhou, T. et al. DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic acids research 41, W56-62 (2013).
Supervisor: PD Dr. Dr. Christian Grimm (Pharmacology, Molecular Biology)
title: Known and novel members of the endolysosomal transportome/channelome as candidates to rescue loss of TRPML1 function in MLIV patients
Aim of this project is to explore novel therapeutic strategies for mucolipidosis type IV (MLIV), a lysosomal storage disorder that is caused by loss or dysfunction of the EL cation channel TRPML1. One focus is on the identification and characterization of surrogates for TRPML1 in the EL channelome/transportome members of which, when specifically stimulated may compensate for the loss of TRPML1 (e.g. two-pore cation channels, CLN proteins, MFSD proteins and others). A second attempt is the identification of small molecule activators/modulators for the afore identified TRPML1 surrogates in high-throughput screens.
Human MLIV patient and wildtype (WT) cells (e.g. fibroblasts) as well as primary murine TRPML1 knockout and WT cells (e.g. neurons) will be used to assess potential rescue effects of putative surrogates for TRPML1 and small molecule activators. Their rescue potential will be analyzed by applying the endolysosomal patch-clamp technique as well as biochemical and microscopy approaches. Finally, the (patho)physiological effects of TRPML1-surrogate proteins and small molecule activators will be assessed in in–vivo experiments. Following validation, identified small molecule activators will be administered to TRPML1 knockout mice and WT mice and will be tested for amelioration of motoric performance, neurological functions and life span.
Grimm C, Jörs S, Saldanha SA, Obukhov AG, Pan B, Oshima K, Cuajungco MP, Chase P, Hodder P, Heller, S (2010) Small molecule activators of TRPML3. Cell Chem. Biol., 17: 135-148
Grimm C, Holdt LM, Chen C-C, Hassan S, Müller C, Jörs S, Cuny H, Kissing S, Schröder B, Butz E, Northoff B, Castonguay J, Luber CA, Moser M, Spahn S, Lüllmann-Rauch R, Fendel C, Klugbauer N, Griesbeck O, Haas A, Mann M, Bracher F, Teupser D, Saftig P, Biel M, Wahl-Schott C (2014) High susceptibility to fatty liver disease in two-pore channel 2-deficient mice. Nature Commun, 5:4699
Chen, C-C, Keller, M, Hess, M, Schiffmann, R, Urban, N, Wolfgardt, A, Schaefer, M, Bracher, F, Biel, M, Wahl-Schott, C, Grimm, C (2014) A small molecule restores function to TRPML1 mutant isoforms responsible for mucolipidosis type IV. Nature Commun, 5: 4681
Sakurai, Y, Kolokoltsov, AA, Chen, C-C, Tidwell, MW, Bauta, WE, Klugbauer, N, Grimm, C, Wahl-Schott, C, Biel, M, Davey, RA (2015) Two pore channels control Ebolavirus host cell entry and are drug targets for disease treatment, Science, 347: 995-998
Supervisor: PD Dr. Ralf Heermann (Microbiology)
Title: Role of AHL-LuxR solos for the life cycle of Photorhabdus bacteria
Bacterial communication to mediate group-coordinated behavior is commonly referred to as quorum sensing. The prototypical quorum sensing system of Gram-negative bacteria consists of a LuxI-type autoinducer synthase that produces acyl-homoserine lactones (AHLs) as signals and a LuxR-type receptor that detects the AHLs to control expression of specific genes. However, many bacteria possess LuxR homologs but lack a cognate LuxI-type AHL synthase. Those LuxR-type receptors are designated as LuxR orphans or solos. Entomopathogenic bacteria of the genus Photorhabdus all harbor an extreme high number of LuxR solos. Two novel quorum sensing systems based on LuxR solos were recently found in Photorhabdus species to regulate cell clumping and therefore pathogenicity. In P. luminescens and P. temperata the LuxR solo PluR senses α-pyrones named photopyrones instead of AHLs, which are produced by the pyrone synthase PpyS. In contrast, P. asymbiotica, a closely related insect and human pathogen, has the PluR homolog PauR, which senses dialkylresorcinols produced by the DarABC pathway to regulate pathogenicity. The plenty of so called PAS4-LuxR receptors are believed to be involved in host sensing. Furthermore, all three Photorhabdus species harbour at least one LuxR solo with an intact AHL-binding motif, which might also allow sensing of exogenous AHLs. Since Photorhabdus bacteria all have a great potential in degrading AHLs, these AHL-LuxR solos could be involved in quorum quenching to block communication of other bacteria. The role of those AHL-LuxR solos for the life cycle of Photorhabdus bacteria, especially for symbiosis and pathogenicity is unknown to date.
Supervisor: Prof. Dr. Kirsten Jung (Microbiology)
Title: Importance of translation elongation factor P (EF-P) for localisation and functionality of membrane-integrated receptors in bacteria
Translation elongation factor P (EF P) functions as an elongation factor and alleviates stalling of ribosomes at polyPro sequence motifs (Ude et al., 2013). This specific function of EF-P was confirmed also for eukaryotes (Doerfel et al., 2013; Gutierrez et al., 2013). EF P is conserved in all bacteria and is orthologous to archaeal and eukaryotic initiation factor 5A (Lassak et al., 2016).
We found that polyPro-induced stalling in combination with EF-P influences the protein copy number of the pH-receptor CadC and hence the cellular stress response (Ude et al., 2013). It is important to note that 11 out of 30 histidine kinase receptors in E. coli contain polyPro motifs, among them EnvZ, EvgS, KdpD and PhoR. It is the aim of the project to analyse the role of the polyPro motifs in these four receptors in protein structure, enzymatic activity, cellular copy number, and stress response, as well as localization and co-localization with their interaction partners in whole cells.
Experience and expertise in microbiological, molecular and bioinformatic techniques as well as a strong interest for microscopic techniques, especially high-resolution microscopy are required.
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
Doerfel LK, Wohlgemuth I, Kothe C, Peske F, Urlaub H, Rodnina MV (2013) EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339:85-88
Gutierrez E, Shin BS, Woolstenhulme CJ, Kim JR, Saini P, Buskirk AR, Dever TE (2013) eIF5A promotes translation of polyproline motifs. Mol Cell 51: 35–45
Lassak J, Wilson DN, Jung K (2016) Stall no more at polyproline stretches with the translation elongation factors EF-P and IF-5A, Mol Microbiol 99: 219–235
Supervisor: Prof. Dr. Heinrich Jung (Microbiology)
Title: Significance and function of SSS family-related signal transduction systems in pathogenic and non-pathogenic Pseudomonas species
The solute/sodium symporter (SSS) family (TC 2A.21, SLC5) comprises integral membrane transport proteins that use an electrochemical sodium gradient to drive the uptake of various organic and inorganic solutes into cells (Jung, 2002). Our previous work focused on the elucidation of the significance and molecular mechanism of function of transporters of this family using a combination of microbiological, biochemical and spectroscopic methods (e.g., (Bracher et al., 2016; Li et al., 2015; Raba et al., 2014).
A new project aims at the characterization of an unusual type of bacterial sensor kinase systems that is characterized by a N-terminal domain which is similar to members of the SSS family (e.g., PanF and PutP) at the structural level while the C-terminal domain shares homology to histidine kinases (e.g., NtrB) (Jung, 2002). Proteins exhibiting such a domain composition are found in proteobacteria of the subgroups alpha, gamma and delta (e.g., the putative proline sensor PrlS of Aeromonas hydrophila, CbrA of Pseudomonas aeruginosa). CbrA functions together with its cognate response regulator, CbrB, and plays an important role in nutrient acquisition (Nishijyo et al., 2001). Recently it was shown that the SSS domain of CbrA of P. fluorescencs is capable of transporting the amino acid histidine (Zhang et al., 2015).
Tasks of the Ph.D. thesis involve the detailed investigation of two different SSS family-related signal transduction systems that are found in both the opportunistic pathogen P. aeruginosa and the soil bacterium Pseudomonas putida. The relevance of these systems for bacterial physiology and virulence shall be explored. Since the mode of action of these systems is still enigmatic, an additional focus of the project will be on the elucidation of the molecular mechanism of function of the sensory systems.
Candidates should have profound knowledge and experimental expertise in microbiological, biochemical and bioinformatic methods and techniques.
Bracher S, Guerin K, Polyhach Y, Jeschke G, Dittmer S, Frey S, Bohm M, and Jung H. 2016. Glu-311 in External Loop 4 of the Sodium/Proline Transporter PutP Is Crucial for External Gate Closure. J Biol Chem 291:4998-5008. doi: 10.1074/jbc.M115.675306
Jung H. 2002. The sodium/substrate symporter family: structural and functional features. FEBS Lett. 529:73-77. doi:
Li Z, Lee AS, Bracher S, Jung H, Paz A, Kumar JP, Abramson J, Quick M, and Shi L. 2015. Identification of a second substrate-binding site in solute-sodium symporters. J. Biol. Chem. 290:127-141. doi: 10.1074/jbc.M114.584383
Nishijyo T, Haas D, and Itoh Y. 2001. The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa Mol.Microbiol. 40:917-931. doi:
Raba M, Dunkel S, Hilger D, Lipiszko K, Polyhach Y, Jeschke G, Bracher S, Klare JP, Quick M, Jung H, et al. 2014. Extracellular loop 4 of the proline transporter PutP controls the periplasmic entrance to ligand binding sites. Structure 22:769-780. doi: 10.1016/j.str.2014.03.011
Zhang XX, Gauntlett JC, Oldenburg DG, Cook GM, and Rainey PB. 2015. Role of the Transporter-Like Sensor Kinase CbrA in Histidine Uptake and Signal Transduction. J Bacteriol 197:2867-2878. doi: 10.1128/JB.00361-15
Supervisor: Prof. Dr. Andreas Klingl ( Plant Development and Electron Microscopy)
Title: Identification and localization of the S-layer proteins of two Acidithiobacillus strains SP5/1 and HV2/2
In course of several studies we could show that the Acidithiobacillus isolates SP5/1 and HV2/2, which belong to the –proteobacteria and are mesophilic and moderate thermophilic, respectively, are covered by a stripe like S-layer protein with p2-symmetry (Klingl et al., 2011). A surface or so called S-layer is a protein, which covers the cell surface and arranges itself in a regular lattice with pseudo-crystalline areas exhibiting either p1-, p2-, p3-, p4- or p6-symmetry driven by a most likely entropic process (Sleytr et al., 2007). Whereas the phylogenetic position of strain SP5/1 as a member of the species Acidithiobacillus ferrooxidans could be clarified (Kelly and Wood, 2000), the status of the isolate HV2/2 is still unclear. It might belong to the species Acidithiobacillus caldus but its ability to oxidize Fe2+ and pyrite might also lead to the description of a new species „Candidatus Acidithiobacillus striatothermus“ angebracht. The main focus of this project will not be the specific phylogenetic status of SP5/1 and HV2/2 but on the common feature of both strains which they also share with other Acidithiobacillus species: the stripe-like S-layer (Fig. 1). Within the project, the protein should be isolated, purified and localized via specific antibodies. The identification of the S-layer protein itself should finally if it shows similarities to Afe_2303 which is mentioned as a potential S-layer protein in the type strain of A. ferrooxidans.
Fig. 1: Transmission electron micrographs of freeze fractured and freeze etched cells of strain Sp5/1 (A-C), HV2/2 (E) and an S-layer deficient lab strain ΔSlp90 (D). Scale bars: 500 nm (A, D, E) and 200 nm (B, C). Also see Klingl et al. (2011).
Kelly D.P. and Wood A.P. (2000). Reclassification of some Thiobacillus to the newly designated genera Acidithiobacillus gen. nov., Halothiobacillus gen. nov. and Thermithiobacillus gen. nov. International Journal of Systematic and Evolutionary Microbiology 50: 511-516.
Klingl A., Moissl-Eichinger C., Wanner G., Zweck J., Huber H., Thomm M. and Rachel R. (2011). Analysis oft he surface proteins of Acidithiobacillus ferrooxidans strain SP5/1 and the new, pyrite-oxidizing Acidithiobacillus isolate HV2/2, and their possible involvement in pyrite oxidation. Archives of Microbiology 193: 867-882. Doi: 10.1007/s00203-011-0720-y
Sleytr U.B., Huber C., Ilk N., Pum D., Schuster B. and Egelseer E.M. (2007). S-layers as a tool kit for nanobiotechnical applications. FEMS Microbiological Letters 267: 131-144.
Supervisor: Prof. Dr. Heinrich Leonhardt ( Cell Biology)
Title: Epigenetic Cancer Evolution
Supervisor: PD Dr. Stylianos Michalakis ( Pharmacology)
Title: Develompment of novel AAV vectors for improved retinal gene therapy
Recombinant adeno-associated virus (rAAV) vectors have become the “gold standard” gene delivery tool for targeting retinal cells. rAAV-based vectors were tested in a number of human clinical trials and have proven safe for the use in the retina. For efficient transduction the current rAAV vector technology requires delivery of the AAV vectors directly to the target cell surface. Direct exposure of the rAAV vectors to the target cell types (retinal photoreceptors) can only be achieved by surgical detachment of the neuroretina from the retinal pigment epithelium (RPE) and delivery of the vectors into this temporally formed subretinal compartment (= subretinal injection). However, subretinal injections result only in a very localized transduction of retinal cells within the subretinal bleb area since (i) AAVs are not able to penetrate well into deeper levels of the retinal tissue and (ii) cells outside the bleb are not exposed to sufficient amounts of the vector.
Therefore, there is a critical unmet need to develop novel AAV vectors with improved transduction properties that enable transretinal gene expression through less invasive routes of delivery (e.g. intravitreal injection).
This projects aims at generating and evaluating using state-of-the-art virological, biochemical, genetic, cell biological and gene transfer methods in relevant in vitro and/or in vivo models (from various species e.g. mouse, dog, pig, NHP, human).top
Supervisor: Dr. Tamara Mikeladze-Dvali (Cell Biology)
Title: The function of centrioles/basal bodies for neurite anchoring during C. elegans mophogenesis
Centrioles carry two main functions: in proliferating cells centrioles recruit peri-centriolar material and act as microtubule organizing centers, which mediate bipolar spindle formation during mitosis; in differentiating cells centrioles become basal bodies and are essential for the formation cilia and flagella (Fig. 1. and 2.). Abnormalities in centriole biogenesis are associated with multiple disorders ranging from microcephaly to ciliopathies and tumor formation. Thus, it is essential that centrioles and basal bodies are tightly regulated according to their cellular context. Our major objective is to uncover molecular mechanisms, by which centrioles and centrosomes are regulated in a tissue specific manner during the development of a multicellular organism.
Sensory neurons in the head of C. elegans, which are born during morphogenesis, form their neurites by a mechanism called retrograde extension. During retrograde extension the ciliary transition zone (or basal body) attaches the tips of the cells at the mouth region of the worm and thereby anchors the neurons (Fig. 3.). The cell body moves away from the anchorage point and consequently the neurite extends (1,2).
The aim of this project is to elucidate the molecular mechanism by which centrioles/basal bodies are targeted to the prospective site of neurite anchoring. Our preliminary data suggest that junctional complexes and polarity factors might be involved in this process. The main goal of the PhD project will be to understand which of these factors are involved in the process of centriole targeting and how exactly centrioles are positioned in prospective location of anchoring. The project will involve a variety of molecular and genetic techniques, as well as imaging using state of the art microscopes.
1. Heiman, M. G. and Shaham, S. DEX-1 and DYF-7 establish sensory dendrite length by anchoring dendritic tips during cell migration. Cell (2009); 137(2)
2. Schouteden, C., Serwas, D., Palfy, M., and Dammermann, A.. The ciliary transition zone functions in cell adhesion but is dispensable for axoneme assembly in C. elegans. J Cell Biol. (2015); 210(1)
Supervisor: Prof. Dr. Jörg Nickelsen (Plant Sciences, Biochemistry, Genetics)
Title: Chlorophyll Incorporation into Photosynthetic Complexes
Thylakoids mediate photosynthetic electron transfer and represent one of the most elaborate energy-transducing membrane systems. Despite our detailed knowledge of its structure and function, much remains to be learned about how the machinery is put together. The concerted synthesis and assembly of lipids, proteins and low-molecular-weight cofactors like pigments and transition metal ions requires a high level of spatiotemporal coordination. While increasing numbers of assembly factors are being functionally characterized, the principles that govern how thylakoid membrane maturation is organized in space are just starting to emerge. In both cyanobacteria and chloroplasts, distinct subcellular production lines for the fabrication of photosynthetic complexes, in particular photosystem II (PSII), have been identified.
In background work, the Nickelsen group has identified OHP2, a member of the LHC superfamily in the green alga Chlamydomonas reinhardtii, as a likely candidate involved in delivering Chl during assembly and/or repair of PSII, in particular to its D1 subunit.
By applying advanced molecular genetics, imaging and biochemical approaches, the suborganellar localization of OHP2, its function during photoprotection, putative interactions partners, and evolutionary conservation will be addressed. Pigment binding and structure of OHP2 will be determined together with international cooperation partners.
Fig.1: PSII assembly and repair in chloroplasts. A possible function of OHP2 in chlorophyll insertion is indicated.
Stengel, A., Gügel, I., Hilger, D., Rengstl, B., Jung, H. and Nickelsen, J. (2012) Initial steps in photosystem II assembly and preloading with manganese take place in biogenesis centers in Synechocystis. Plant Cell 24, 660-675.
Nickelsen, J. and Rengstl, B. (2013) Photosystem II assembly: From cyanobacteria to plants. Annu. Rev. Plant Biol. 64, 609-635.
Bohne, A.-V., Schwarz, C., Schottkowski, M., Lidschreiber, M., Piotrowski, M., Zerges, W. and Nickelsen, J. (2013) Reciprocal regulation of protein synthesis and carbon metabolism for thylakoid membrane biogenesis. PLoS Biol. 11, e1001482.
Rast, A., Heinz, S., Nickelsen, J. (2015) Biogenesis of thylakoid membranes. Biochim. Biophys. Acta, DOI: 10.1016/j.bbabio.2015.01.007. [Epub ahead of print].
Supervisor: Prof. Dr. Kai Papenfort (Microbiology)
Title: Autoinducer-controlled riboswitches in commensal and pathogenic bacteria
Quorum sensing (QS) is the process of cell-cell communication among microbes (1). QS involves the production, release, and detection of extracellular signaling molecules called autoinducers, and allows bacteria to collectively regulate gene expression in response to changes in cell density and species composition of the vicinal community. Many, if not all, bacteria use QS to regulate gene expression, and this process is intimately linked to pathogenesis and biofouling (2). Understanding QS is fundamental to all of microbiology, and ultimately could prove to be key to understanding other collective behaviors, including those of higher organisms.
In all cases known to date, autoinducers bind to cognate protein receptors, which are either transcription factors or signaling proteins. In this project, we aim to identify and characterize natural RNA molecules, i.e. riboswitches, directly interacting with bacterial autoinducers. Riboswitches are bi-modular RNAs that are made up of a ligand-binding sequence (an aptamer) and an expression platform that controls gene production (3). Typically, riboswitches are located in the 5’ untranslated regions of mRNAs, where they control gene expression by binding to low molecular weight molecules that trigger a conformational shift in the RNA. Gene expression control through riboswitches is highly dynamic and provides exquisite temporal control.
In this project, the PhD student will employ state-of-the-art RNA sequencing technology (4) to discover RNA-elements responsive to one or several autoinducers. Follow-up experiments will aim at the understanding of the molecular mechanisms underlying this process. RNA regulators, and specifically riboswitches, have recently been established as potent drug targets. Consequently, riboswitches responding to autoinducers, or autoinducer mimics, could become important toeholds to potentiate and diversify antibacterial therapies targeting quorum sensing.
1. Papenfort, K. and Bassler, B.L. (2016) Quorum-Sensing Signal-Response Systems in Gram-Negative Bacteria. Nat Rev Microbiol, in press.
2. Dong, Y.H., Wang, L.H., Xu, J.L., Zhang, H.B., Zhang, X.F. and Zhang, L.H. (2001) Quenching quorum-sensing-dependent bacterial infection by an N-acyl homoserine lactonase. Nature, 411, 813-817.
3. Serganov, A. and Nudler, E. (2013) A decade of riboswitches. Cell, 152, 17-24.
4. Papenfort, K., Forstner, K.U., Cong, J.P., Sharma, C.M. and Bassler, B.L. (2015) Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Proc Natl Acad Sci U S A, 112, E766-775.
Supervisor: Prof. Dr. John Parsch (Evolutionary and Functional Genomics)
Title: Gene regulatory variation in Drosophila melanogaster
Differences in gene expression are thought to underlie many of the phenotypic differences between species and populations. Transcriptomic technologies, such as high-throughput RNA sequencing (RNA-seq), have made it possible to identify the genes that vary in expression among individuals of a species. This project studies gene expression variation within and between populations of the fruit fly Drosophila melanogaster, a species that has its origin in sub-Saharan Africa and only relatively recently has become a successful colonizer of other word-wide habitats. In order to better understand the role of gene regulatory changes in adaptation, both genome-wide and candidate-gene studies will be carried out. The goal is to identify specific genetic polymorphisms that underlie gene expression variation and to determine the population genetic mechanisms that are responsible for maintaining them in natural populations. A further goal is to determine the effect that variation in gene expression has on an organismal phenotype that may be subject to natural selection.
Catalán A., A. Glaser-Schmitt, E. Argyridou, P. Duchen, and J. Parsch (2016) An indel polymorphism in the MtnA 3' untranslated region is associated with gene expression variation and local adaptation in Drosophila melanogaster. PLoS Genet. 12(4):e1005987.
Huylmans, A. K., and J. Parsch (2014) Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster.G3 (Bethesda) 4: 2307-2315.
Glaser-Schmitt, A., A. Catalán, and J. Parsch (2013) Adaptive divergence of a transcriptional enhancer between populations of Drosophila melanogaster Phil. Trans. R. Soc. B 368: 20130024.
Supervisor: PD. Dr. Serena Schwenkert (Plant Sciences)
Title: Chaperones and TPR proteins in organellar protein import and chloroplast biogenesis
In the eukaryotic cell most organellar proteins are synthesized as preproteins in the cytosol and are either post- or co-translationally translocated into chloroplasts, mitochondria or the endoplasmic reticulum. During posttranslational protein transport the preproteins have to be kept in an import competent state and molecular crowding has to be prevented, since this can easily lead to misfolding or aggregation. This process is assisted by the molecular chaperones HSP90 and HSP70, which also mediate interaction of preproteins with the membrane surfaces. This interaction is conferred by tetratricopeptide repeat (TPR) proteins, which are associated with the translocon complexes. The aim of this project is to characterize the molecular and regulatory function of these TPR docking proteins during posttranslational protein transport. The functional and structural analyses of these docking proteins will not only provide insight into the import mechanism of preproteins but also elucidate the role of chaperones and the respective receptors in specific targeting of preproteins. Moreover, not only the cytosolic, but also the chloroplast resident TPR proteins as well as HSP90 are indispensable for chloroplast biogenesis. We will therefore investigate the composition and mode of action of the chloroplast HSP90 machinery, with special focus on its conformational dynamics in comparison with the cytosolic localized chaperone setup. To this end we will apply a variety of biochemical and molecular biological techniques, such as protein purification, co-immunoprecipitation and expression of fluorescent proteins.
For further information see: http://www.en.botanik.bio.lmu.de/research/soll/subgroups/schwenkert/index.html
Supervisor: Dr. Esther Zanin (Cell Biology)
Title: Molecular mechanisms controlling polar body cytokinesis
During meiosis the diploid genome is segregated into haploid gametes. If meiosis fails, the embryo will inherit an abnormal chromosome number and die. Infertility in humans is often caused by defects in meiosis and therefore understanding the molecular mechanisms of meiosis will help to develop novel therapeutic strategies to treat infertility. Female meiotic divisions are highly asymmetric generating two small polar bodies and a large ovum1. One great model system to study female meiosis is the small nematode C. elegans since fertilized embryos can be easily obtained for live-cell microscopy and many molecular and genetic tools are well established in this model organism.
Like in vertebrates, in C. elegans the meiotic spindle aligns perpendicular to the plasma membrane during metaphase (Fig. 1). Firstly, the cell cortex adjacent to the spindle pole is remodeled and a premature contractile ring assembles2. Secondly, in anaphase the contractile ring ingresses from the cell surfaces along the meiotic spindle. Than contractile ring ingression stops half way between the segregating chro-mosomes at the spindle midzone. Finally the contractile ring constricts and the polar body is abscised. To ensure the correct segregation of the genetic content the ingression and constriction of the contractile ring as well as the abscission of the polar body has to be spatially and temporally coordinated with chromosome segregation and cell cycle progression. How this complex control is achieved on the molecular level is only poorly understood at present and the PhD project will address this question. During mitotic cytokinesis the molecular pathways that control contractile ring formation are well established3. Mitotic and meiotic cytokinesis share many similarities but they also differ: for example, in mitotic cytokinesis contractile ring formation is induced in anaphase but not in metaphase. Further the mitotic anaphase spindle has centrosomal microtubule asters whereas the meiotic spindle is acentriolar. It has been shown that some mitotic cytokinesis regulators are required for polar body cytokinesis2,4 however at which step and how they function has not been determined. Due to the morphological differences between meiotic and mitotic cytokinesis it is likely that the communication between the spindle and the cell cortex also differs. The goal of our laboratory is to reveal the regulatory network that controls cytokinesis during cell division. Towards this goal we combine several complementary approaches in the nematode C. elegans and human tissue culture cells. We aim to identify signaling complexes involved in cytokinesis by biochemical approaches as well as by genome-wide microscopy-based screens. Signaling complexes involved in cytokinesis often have multiple functions during the cell division. To disrupt their function specifically during cytokinesis or in a specific region of the cell we will also develop light-controllable compounds in collaboration with the group of H. Dube. The function of the identified signaling complexes is than investigated in vivo by quantitative live-cell microscopy. The proposed PhD project will use a variety of microscopy-based, biochemical and screening techniques to dissect the molecular pathways controlling polar body cytokinesis.
1. Maddox, A. S., Azoury, J. & Dumont, J. Polar body cytokinesis. Cytoskeleton (Hoboken) 69, 855–868 (2012).
2. Dorn, J. F. et al. Actomyosin Tube Formation in Polar Body Cytokinesis Requires Anillin in C. elegans. Current Biology 20, 2046–2051 (2010).
3. Green, R. A., Paluch, E. & Oegema, K. Cytokinesis in Animal Cells. Annu. Rev. Cell Dev. Biol. 28, 29–58 (2012).
4. Fabritius, A. S., Flynn, J. R. & McNally, F. J. Initial diameter of the polar body contractile ring is minimized by the centralspindlin complex. Developmental Biology 359, 137–148 (2011).top