Doctoral Researchers

 
Häder, Antje

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
ZIK Septomics
Research Group Fungal Septomics
PhD Project:

Genome-wide identification of risk markers during the immune response towards pathogens of systemic infections

 
 
Hanf, Benjamin

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ILRS Student

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Dept. Molecular and Applied Microbiology
PhD Project:

Low temperature stress of filamentous fungi

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Abstract: Fungi naturally encounter sharp temperature shifts in their environment. In this context, some fungi have evolved protective mechanisms to be more resistant against low temperatures....
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... Further on, silent gene clusters can be induced due to the initiation of new stress factors. Little is known about the adaptation to cold and cryo stress in Ascomycetes. To identify the key processes induced at low temperatures, the proteome such as the secondary metabolite production of the well-studied filamentous fungus Aspergillus nidulans was analyzed under defined cold stress conditions in a comparative gel-based (DIGE) and gel-free (LC-MS/MS) proteomic approach. Further on, the formation of secondary metabolites will be identified by LC-MS/MS. Another focus of this study will be the investigation of post-transcriptional changes, particularly the acetylome, which is currently completely unknown for the species Aspergillus. First insights should be provided into the regulation of different proteins in A. nidulans after inducing cold stress. In addition, different experimental methods should be combined to develop an improved identification of activated secondary metabolite biosynthesis gene clusters. This work will be complemented by transcriptional profiling of the cold stress response in A. nidulans. Interesting genes or proteins will be further analyzed by molecular biological techniques. Most likely, the generated data may support the development of new approaches to optimize the cryopreservation of fungi and may reveal putative anti-freezing-proteins or new osmoprotectants which could lead to an advanced long-term storage of fungi or other organisms.
 
 
Heinrich (né Raszkowski), Daniel

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Pharmacy
Pharmaceutical Biology I
PhD Project:

Evolution of glorin-based intercellular communication in social amoebae

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Abstract: The “social amoebae” are a group of unicellular organisms that transiently achieve multicellularity by aggregation of single cells, aimed at the formation of fruiting bodies whose...
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... spores survive environmental conditions unfavorable for growth. Multicellular development of social amoebae is accompanied by intensive intercellular communication, which has to some extent interesting parallels with bacterial quorum-sensing and quorum-quenching systems. Extracellular signaling molecules used by social amoebae to coordinate aggregation of usually reffered to “acrasins” irrespective of their chemical natures. A hallmark or amoebal acrasin systems is that the signaling molecule is periodically degraded, which allows the amoebae to position in an acrasin gradient and move to the highest concentration of the signaling molecule, which is the aggregation center. Thus, besides the signaling molecule and its receptor, an acrasin system of social amoebae requires a self-produced and secreted enzyme that inactivates the acrasin. Several of the species that diverged late in the evolution of social amoebae use cAMP to regulate aggregation. In this project we follow the hypothesis, based on our previous work, that the phylogenetically oldest species of social amoebae use the modified dipeptide glorin instead of cAMP as the intercellular signaling molecule that coordinates aggregation. In addition, we assume that glorin is secreted by cells of genus Polysphondylium and that these species produce an enzyme (a “glorinase”) that is capable of inactivating glorin in the extracellular space. A major goal of this project is to identify the glorinase-encoding gene from Polysphondylium pallidum. To this end, we will establish a biochemical assay to measure glorinase activity in the buffer supernatant of aggregating P. pallidum cells. This assay will be fundamental to purify extracellular glorinase from aggregating P. pallidum cells by activity-guided fractionation. The glorinase protein will be identified by means of proteomic methods and this information will be used to identify the glorinase gene in the P. pallidum reference genome. To explore the function of glorinase in coordinating P. pallidum aggregation, we will generate a knock-out mutant of glorinase in P. pallidum. This mutant will be characterized in terms of developmental phenotypes. A detailed expression of the glorinase gene will answer the question how the gene is regulated at the transition from growth to development of P. pallidum cells. Search for functional glorinase orthologs in other sequenced genomes of social amoebae will shed light on the evolution of the glorin-based communication system in social amoebae as well as on the origin of ths system and its relation to bacterial quorum-sensing systems.
 
 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Bio Pilot Plant
PhD Project:

Optofluidic study and characterization of microbial communities in a novel droplet-based microfluidic system with integrated optical fibers

 
 
Institute/Dep.
Friedrich Schiller University Jena
Institute for Materials Science and Technology (IMT)
PhD Project:

TFP TV9

 
 
Hermenau, Ron

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ChemBioSys Student

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Dept. Biomolecular Chemistry
PhD Project:

Chemical Mediators in the Interaction between Bacteria and Plants/Fungi

 
 
Hirth, Matthias

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Matthias Schleiden Institute
Junior Research Group 'Molecular Botany'
PhD Project:

The metabolic profile of the marine microalga Ostreococcus tauri

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Abstract: With its cosmopolitan distribution and capability to form blooms, the unicellular marine alga Ostreococcus is of ecological significance [1]. Since it has a small diameter (ca. 1...
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... Mikrometer) and genome size (12.6 Mb), it has been speculated that O. tauri may represent a minimal version of a photosynthetic eukaryote [1]. At the metabolic level, Ostreococcus is hardly characterised to date. In the first part of this project, the metabolic profile of O. tauri will be described under different growth conditions. These conditions include growth under constant light, light-dark cycles, circadian conditions and iron starvation. In collaboration with Georg Pohnert (Friedrich Schiller University, Jena), cellular extracts will be analysed by gas chromatography coupled with mass spectrometry (GC-MS) by exploiting a newly devised protocol [2]. This method involves derivatisation by methoxymation/silylation, which enables the detection of a variety compounds such as amino acids, fatty acids, alcohols or sugars. Compounds will be identified by matching mass-spectrometric fragmentation patterns with database entries, and interesting compounds will be confirmed by comparison with a standard. The results will lay the foundation for further metabolic investigations in Ostreococcus. In the second part of this project, the metabolic profiles of various O. tauri regulatory mutants will be examined and compared to the profile of the wild type. Mutants will be obtained from François-Yves Bouget (Observatoire Océanologique in Banyuls-sur-Mer, France). The characterisation of these mutants at the physiological and metabolic levels will elucidate how regulatory networks control metabolism in O. tauri. This project is an essential step to understand how this ecologically important alga adapts to changes in environmental conditions, and to engineer algae for biotechnological applications such as the production of high-value compounds. [1] Derelle, E., et al., Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl. Acad. Sci. U. S. A. 103, 11647-11652 (2006). [2] Vidoudez, C. and G. Pohnert, Comparative metabolomics of the diatom Skeletonema marinoi in different growth phases. Metabolomics 8, 654-669 (2012).
 
 
Hoang, Mai

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JSMC Fellow

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Institute/Dep.
University Hospital Jena
Department for Internal Medicine II
Haematology and Medical Oncology
PhD Project:

Characterisation of Aspergillus fumigatus mutants regarding their interaction with human leucocytes

 
 
Hsieh, Shih-Hung

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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
Microbial Biochemistry and Physiology
PhD Project:

Interaction of Aspergillus terreus with dendritic cells

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Abstract: Dendritic cells, professional antigen presenting cells, are important immune cells to turn on adaptive immune responses on the one hand and provide innate immune protection on the other...
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... hand. Upon phagocytosing pathogens, dendritic cells become active to produce inflammatory cytokines and migrate to draining lymph nodes, which directly leads to T cell cytokine production. In a later phase it also leads to antibody secretion by B cells. Fungal pathogens appear largely recognized by dendritic cells through pattern recognition receptors such as TLR2, TLR4, mannose receptor and dectin-1. This further triggers dendritic cell maturation and migration during fungal infection. In our previous studies, we showed that Aspergillus terreus and Aspergillus fumigatus present different levels and compositions of cell wall antigens and display different survival strategies after phagocytosis by macrophages. Aspergillus fumigatus hides from phagocytosis, tends to inhibit acidification of phagolysosome and escapes by macrophage piercing hyphae. By contrast, Aspergillus terreus is rapidly phagocytosed by increased exposure of beta-1,3-glucan and galactomannan on the surface. Furthermore, phagolysosome acidification is not inhibited and conidia remain trapped in a resting albeit viable state. Although both, macrophages and dendritic cells, are antigen presenting cells they can show differences in their specific immune reactions even to the same pathogen. During A. fumigatus infection, dendritic cells become activated and express co-stimulated molecules and inflammatory cytokines. Due to the inactive behavior of A. terreus in macrophages, this response is much less pronounced. Thus, we believed that A. terreus may also display different strategies during the interaction with dendritic cells. To address this issue, monocyte-derived dendritic cells will be studied for their specific response towards A. fumigatus and A. terreus to analyze their impact in combating infection.