Doctoral Researchers

 
Papanikolopoulou, Lydia

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute for Inorganic and Analytical Chemistry
PhD Project:

Mechanisms of positive allelopathy in phytoplankton

 
 
Peña Ortiz, Luis Alberto

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Institute/Dep.
Friedrich Schiller University Jena
Carl Zeiss Junior Research Group Synthetic Microbiology
PhD Project:

Identification and biotechnological assembly of cryptic cofactors

 
 
Pezzini, Francesco

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JSMC Fellow

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Research Group: Systems Biology / Bioinformatics
PhD Project:

Epigenetic control of secondary metabolism in filamentous fungi (Bioinformatic analysis and modeling)

Abstract: Secondary metabolites (SM) (antibiotics, toxins, etc.) are pharmaceutically important substances involved in microbial communications. The PhD project will be devoted to detection of...
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... epigenetic marks for regulation of SM cluster genes. This will include the work with NGS data (e.g., merging nucleosome and transciptome data), analysis of nucleosome positioning in genes and promoters of active and inactive SM clusters, application of comparative analysis and systems biology approaches
 
 
Phieler, René

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GRK1257 Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Microbiology
Microbial Communication
PhD Project:

Microbially supported phytoremediation of the heavy metal contaminated site Gessenwiese

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Abstract: The increasing release of heavy metals to the environment due to anthropogenic activities such as mining operations and smeltering is a serious problem world-wide. Microbially...
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... supported phytoremediation may be viewed as potentially useful approach. Soil bacteria and mycorrhizal fungi can alter physico-chemical properties in the rhizosphere and may alter soil metal bioavailability for uptake into plants. This project will focus on studying remediation potential of selected plants at the heavy metal contaminated site Gessenwiese, located on the basement of the former uranium leaching heap Gessenhalde near Ronneburg, Thuringia. The objective is to develop more knowledge-driven field remediation techniques to remediate and restore contaminated sites. Of special interests are the interactions between soil microorganisms and plants with respect to the uptake of heavy metals. Field experiments as well as pot experiments will be carried out in order to assess the effects of microbial inoculation on biomass production and total uptake of heavy metals by host plants.
 
 
Pietschmann, Sebastian

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Microbiology
Microbial Communication
PhD Project:

Microbial succession in heavy-metal contaminated soils during in-situ phytoremediation

 
 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Dept. Microbial Pathogenicity Mechanisms
PhD Project:

The role of morphology for fungal pathogenicity

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Abstract: The pathogenic fungus Candida albicans is able to colonize many different body sites and infections range from harmless superficial lesions up to severe and life threatening...
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... disseminated candidiasis. For the invasion and tissue penetration process of the fungus the transition from the spherical yeast to the filamentous hyphal growth form is essential. In addition to adhesion and invasion hyphae also mediate the escape from host cells such as endothelial cells and macrophages after internalization. Since the yeast-to-hypha transition is of great importance for the development of disease it is not surprising that this process is tightly regulated by a complex network of both positive and negative regulatory factors. While the knowledge about regulatory mechanisms controlling morphogenesis is rising, the exact role of morphology for the pathogenicity of C. albicans is still not fully clear. Studies revealed that not all filament-deficient mutants are attenuated in virulence, indicating a more complex relationship between morphology and infection process. Therefore the aim of this project is to analyze the contribution of different regulators of filamentation to pathogenesis and host-pathogen interaction. To analyze these regulators in a comparable genetic background, strains carrying the gene of interest under a doxycycline-inducible promoter will be constructed. These strains will then be analyzed in detail for filamentation defects, expression of virulence-associated factors and interaction with different host cells in vitro. Furthermore, different in vivo models will be used to determine the impact of the genes of interest on the various aspects of the host-pathogen interaction in complex systems.
 
 
Pötschner, Jessica

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Microbiology
Microbial Communication
PhD Project:

Lipid rafts in fungi

 
 
Pourmasoumi, Farzaneh

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JSMC Fellow

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute -
Junior Research Group
Biosynthetic Design of Natural Products
PhD Project:

Directed evolution of antibiotic producers

 
 
Preußger, Daniel

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JSMC Fellow

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Institute/Dep.
Max Planck Institute for Chemical Ecology
Dept. of Bioorganic Chemistry
PhD Project:

The evolution of metabolic cooperation within bacterial communities: causes and consequences

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Abstract: Bacteria live in diverse communities and frequently interact by the exchange of metabolites. However, those cooperative interactions pose a conundrum to evolutionary biology: costly...
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... benefits directed to other cooperating individuals are vulnerable to be undermined by selfish mutants, which gain a selective advantage by not reciprocating. Despite this seeming conflict, cooperation within and between different bacterial species is very common and plays a vital role in many ecosystems. Therefore, conditions, promoting the evolution and maintenance of such interactions, are worthwhile to be investigated: These are in detail ecological factors, co-evolutionary trajectories and consequences of metabolic capabilities within interacting species. To study effects of these parameters, long-term coevolution experiments will be performed under varying ecological conditions. Precisely defined bacterial consortia are allowed to develop metabolic cooperation, initially starting from a synthetically engineered obligate by-product interaction based on amino acid auxotrophies. A well-established analysis pipeline, in which the derived consortia are analysed for genetic and phenotypic changes that occurred during the selection experiments, will then help to causally link different initial conditions to the observed evolutionary outcomes. Evolved cooperation will be characterised by analysing fitness relative to ancestors, local adaptation, and frequency dependent selection of partners. In this way, several hypotheses on the causes and consequences of metabolic cooperation within bacterial communities can be scrutinized.
 
 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Dept. Molecular and Applied Microbiology
PhD Project:

Molecular mechanisms of antifungal resistance and therapeutic strategies to manage infections with triazole

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Abstract: The PhD project in the group of Prof. Dr. Brakhage (Department of Molecular and Applied Microbiology) studies the human pathogenic fungus Aspergillus fumigatus and consists of two...
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... parts. One part belongs to the FINAR (Management of Fungal Infections in the Era of Emerging Azole Resistance) effort and focuses on the emerging problem of azole antifungal resistance in filamentous fungi. This topic is currently very important as more and more azole-resistant fungal isolates are recovered from patients, but there are very few treatment alternatives. The starting point for this project are natural products which show a synergistic effect when applied together with azole antifungals. These compounds could be the first step towards drugs that preserve the activity of azole antifungals in spite of the emerging resistances. The aim of this project is to characterize the effect and the mechanism of action of these compounds using –omics methods and a Knock-Out-mutant library of A. fumigatus and to possibly find new resistance mechanisms. The second part of the PhD project is aimed at DHN-melanin, a virulence factor of A. fumigatus. DHN-melanin is located on the conidial surface and protects the conidia for example against UV radiation and, during infection, from host defense mechanisms. It can withstand even harsh conditions easily. This project aims to discover how DHN-melanin is degraded by the fungus using proteomic and transcriptomic approaches.