Doctoral Researchers

 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Bio Pilot Plant
PhD Project:

Exploiting the metagenome of microbial communities on a microfluidic platform

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Abstract: In the course of this dissertation a surfactant-based microfluidic platform is employed to discover new bioactive natural products. Due to the failure of the recently predominant...
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... target-oriented screening approaches we intend to use a whole-cell-based screening method. To test for the synthesis of natural products within the droplets, we utilize reporter cells that ideally indicate antimicrobial activity, using constitutive or stress-inducible promoters. Three different strategies are envisaged. In one approach, we plan to exploit complex mixtures of antibiotic producers derived from different habitats like soil and sea water with laying the focus on yet uncultivated or slow growing actinomycetes. Second, the system can be applied in the research of silent gene clusters revealed by genome mining of characterized bacterial strains. This will be realized by cultivating a single strain of Actinobacteria under highly variable culture conditions implemented by media gradients during droplet generation. A third envisioned approach is to screen a combinatorial library of oligopeptides with putative antimicrobial activity (provided by Prof. Dr. Wiesmüller EMC microcollections GmbH, Tübingen). After detection of droplets with inhibited reporter strains the respective amino acid sequence can be elucidated by mass spectrometry analysis.
 
 
Mamerow, Svenja Katharina

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Institute/Dep.
PhD Project:

Development and Evaluation of Influenza A Virus Live Attenuated Vaccines in Swine

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

Characterizing innate immune cell activation by fungal pathogens using Live Cell Imaging

 
 
Marx, Carina

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Institute/Dep.
PhD Project:

Identifizierung molekularer Targets potentieller Antibiotika

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

Using fluorescent Enterococcus mundtii to study the variation in its gene expression, spatially and temporally, in the gut of Spodoptera littoralis larva

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Abstract: Insects harbor a plethora of microorganisms within their gut, as their normal flora. They are not only non-pathogenic to them, but also have roles to play in the insect growth,...
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... development and immunity. There lies a complex interaction within the microflora and also, between the host and the microorganisms. This leads to variations in the microbial population with the development of the insect. Some get eliminated, some are added, whereas, some dominate throughout the insect life cycle. The gut microbiota of Spodoptera littoralis, a Lepidopteran insect of family Noctuidae, has been elucidated. The core community consists of Enterococci, Lactobacilli and Clostridia. The selection of one bacterial species over the other is quite evident throughout the life-cycle. The community varies with the stages of development of the larva, and spatially within the gut. By the time the larva reaches the 5th instar stage, Enterococcus mundtii and Clostridia sp persists and dominates. The class IIa antimicrobial peptide- mundticin KS, produced by Enterococcus mundtii, acts against the invading bacteria, and exercises its predominance. This way, they help preserve the host gut microbiota, reduce infection in the host and enhance its health. A method of fluorophore-labelling of Enterococcus mundtii has been developed to show that it is the persistent and metabolically active species in the gut microbiota, which in turn, intrigues us to find out the importance of this symbiotic species. Thus, the aim of my project will be to isolate the fluorescent Enterococcus mundtii from various regions of the larval gut, across its developmental stages, and study the variation in their gene expression. The Next generation method of RNAseq will be used to sequence the transcriptome. Thus, on analyzing the transcriptome of Enterococcus mundtii over the stages of Spodoptera littoralis larval development, we might conclude its specific role as a symbiont and its importance as a dominating gut microbiota. Once successful, the approach can be extended to other relevant gut bacteria and their role as symbionts, like, Clostridia sp, which dominate the gut till the later stages of development, even in depleting iron conditions.
 
 
Meichsner, Doreen

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of General Botany and Plant Physiology
Dept. of Plant Physiology
PhD Project:

Symbiosis-specific exudate components from the beneficial root-colonizing fungus Piriformospora indica and Arabidopsis thaliana

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Abstract: In this project, we will study the beneficial interaction between the root-colonizing fungus Piriformospora indica and the model plant Arabidopsis thaliana. The endophytic fungus P....
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... indica colonizes of the roots of many plant species. Similar to arbuscular mycorrhizal fungi, P. indica promotes plant growth, biomass and seed production and confers resistance to biotic and abiotic stress (Shahollari et al., 2007, Vadassery et al., 2009, Camehl et al., 2011, Nongbri et al., 2012, and references therein). P. indica is a member of Sebacinales, grows inter - and intracellularly and forms pear shaped spores, which accumulate within the roots and on the root surface. After the establishment of a beneficial interaction, barely any defense or stress genes are activated and no reactive oxygen species are produced by the host against P. indica (Camehl et al., 2011). The endophyte releases a small compound into the medium/rhizosphere which induces root-specific [Ca2+]cyt elevation in Arabidopsis and N. tabacum. [Ca2+]cyt elevation is followed by a nuclear Ca2+ response (Vadassery et al., 2009), similar to signalling events in arbuscular mycorrhizal fungi.
Using established cultivation and co-cultivation conditions, we will try to identify proteins, peptides and other biomolecules which are released from the two partners into the medium. Comparative analyses of the secretomes and metabolomes (released by the microbial and plant partners alone and in symbiotic interaction between the two partners) should identify those compounds which are symbiosis-specific. Since the genomes of both organisms are sequenced and available, the origin of the proteins and peptides can be identified. Furthermore, genome mining should help to identify the origin and biosynthesis of the symbiosis-specific biomolecules.
 
 
Meyer, Nils

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ChemBioSys Student

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

Algicidal Bacteria in Plankton Communities: Resistance, Lysis and Heterotrophy

 
 
Mohr, Jan Frieder

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ChemBioSys Student

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

Metallophores as mediators for metal cycling: Development of libraries for metal ion buffering and as redox carriers as well as profiling of metallophores

 
 
Müller, Tina

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JSMC Fellow

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Institute/Dep.
University Hospital Jena
Clinic of Anaesthesiology and Intensive Care Medicine
Research Unit Experimental Anesthesiology
PhD Project:

Host defense mechanisms against pathogens mediated by sphingolipids

 
 
Munser, Anne-Sophie

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Institute/Dep.
Fraunhofer Institute for Applied Optics and Precision Engineering, Jena