Doctoral Researchers

 
Schaarschmidt, Barbara

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FungiNet Student

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

Effects of hypoxia and intestinal nutrients on intestinal barrier function and translocation of microorganisms

Abstract: The transition of C. albicans from a commensal within the gut to an invasive pathogen is of great clinical importance. However, it is largely unknown which host factors trigger the...
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... transition and which fungal factors are essential for translocation through the gut. There is experimental evidence that intestinal ischemia/hypoxia, e.g., during major surgery and shock/sepsis, weakens the intestinal barrier and may promote translocation of C. albicans. We furthermore hypothesise that the environmental alterations during intestinal hypoxia trigger a specific fungal response that is associated with increased translocation. The aim of this project is to dissect the translocation process with regard to the involved anatomical sites and host cells, immune response and fungal factors. Furthermore, the effect of intestinal ischemia/hypoxia on C. albicans translocation will be evaluated. In vitro cell culture experiments will be used to determine intestinal cell barrier functions under different levels of hypoxia and the consequences for interaction with C. albicans. Transcriptional analysis will be used to identify pathways involved in epithelial response to hypoxia and fungal factors contributing to the interaction. The obtained results will be confirmed in murine ex vivo and in vivo models. To determine at which anatomical sites translocation occurs and which host cells are involved, a murine in vivo model of dissemination from the gut will be established and analysed by using fungal reporter strains and imaging (IVIS), determination of fungal burden, histology and immunhistochemistry, FACS and cytokine ELISAs. To test the hypothesis that intestinal ischemia/hypoxia enhances translocation of C. albicans through the gut, the consequences of intestinal hypoperfusion on the colonisation and translocation of C. albicans will be tested in an ex vivo model using externally perfused gut and in vivo. Transcriptional analyses as well as loss-of-function models of both host and fungus will be used to identify factors involved in the translocation process under normoxia and hypoxia in vivo. Furthermore, the transcriptional analyses allow determine whether intestinal ischemia/hypoxia leads to a specific fungal response involved in translocation. Finally, based on the transcriptome analysis and on barcoded mutant libraries, C. albicans mutants will be tested for their translocation potential to identify fungal factors essential for translocation.
 
 
Schädel, Kristina

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JSMC Fellow

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

Pea aphids and their facultative bacterial endosymbionts: exploring the occurrence, effects and mechanism of a widespread symbiosis

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Abstract: Insects, like virtually all other groups of animals, have established many mutualistic associations with microbes. Herbivorous insects, in particular, harbor a large diversity of...
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... endosymbiotic bacteria in their bodies that have been found to increase insect growth, development and survival. However, how these bacteria actually improve insect performance is often not understood. Endosymbionts may supplement essential nutrients in the insect diet, digest recalcitrant plant polymers, degrade plant defense compounds or act in some other way. Knowledge of the specific benefits provided by endosymbiotic bacteria should shed more light on the biological importance of these widespread associations and also suggest novel methods for controlling insects that are agricultural or forest pests. In our research group, we have long used one insect taxon, the pea aphid (Acyrthosiphon pisum), as a model for investigating species formation in insect herbivores. We seek to understand why over half of the earth’s terrestrial species (excluding microbes) are herbivorous insects. The pea aphid is composed of at least 15 distinct host races, each specialized on a different range of plants of the legume family. All aphids ingest phloem sap, which while rich in carbohydrates is deficient in many nitrogen-containing compounds. For this reason, all aphids contain an obligate bacterial endosymbiont, Buchnera aphidicola (Gammaproteobacteria), housed in specialized cells near the midgut, which provides essential amino acids. In addition to their obligate endosymbiont, many pea aphids are reported to also contain other bacteria as facultative endosymbionts, including strains of Regiella and Serratia (Gammaproteobacteria) and Rickettsia (Alphaproteobacteria). These microbes are located in many parts of the aphid body, but their biological roles are much less clear than those of the obligate endosymbiont. We have been investigating these facultative endosymbionts of the pea aphid to see if they might be associated with host plant specificity. Intriguingly, we found that Regiella associated with aphids living on clover significantly increased the performance of pea aphids on this host plant, and now wish to explore how this bacterium triggers such improvements in insect performance. Our preliminary results suggest that Regiella-harboring pea aphids modify plant hormone levels in clover and thus might actually be able to suppress the accumulation of plant defenses. We propose to determine the importance of the association between Regiella and the pea aphid by: (1) surveying the distribution of this facultative bacterial endosymbiont in pea aphid populations on different host plants, (2) assessing its effects on feeding behavior, growth, reproduction and survival, and (3) determining how Regiella influences the suitability of the host plant for the aphid. Knowledge of the biological significance and mechanism of this widespread symbiosis may reveal a new dimension in insect-microbe interactions as well as explain the diversity of host plant associations in the pea aphid complex. Moreover, information about how Regiella helps aphids overcome plant defenses could be useful in designing new measures to combat one of the world’s major groups of grain, vegetable and fruit pests.
 
 
Schaeme, Daniel

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ChemBioSys Student

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Institute/Dep.
Friedrich Schiller University Jena
Matthias Schleiden Institute
Dept. of Plant Physiology
PhD Project:

Identification of Novel Secondary Metabolites with Roles in Interactions Between Chlamydomonas reinhardtii and Other Microorganisms

 
 
Scheven, Mareike

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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:

Novel molecular mechanisms of iron sensing and homeostasis in Aspergillus fumigatus

 
 
Schmidt, Franziska

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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:

Virulence of Aspergillus fumigatus and Host-Pathogen Interactions

 
 
Schumann, Martin

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Geosciences
Mineralogy & Geochemistry
PhD Project:

Microbial origin of banded iron formations

 
 
Schürmann, Michaela

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

Antimicrobial Effect of Nano-Rough Titanium surfaces: Reduction of Microbial Adhesion and Mechanisms of Reduction

 
 
Shen, Haodong

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JSMC Fellow

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Physical Chemistry
PhD Project:

Photonics as a non-destructive investigation strategy for biofilms

 
 
Institute/Dep.
Friedrich Schiller University Jena
Dept. of Bioinformatics
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Research Group: Systems Biology / Bioinformatics
PhD Project:

Bioinformatic Analysis of alternative splicing in human pathogenic fungi

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Abstract: Alternative splicing (AS) processes can be found in a wide range of species. It is well studied in higher organisms but little is known about its regulation and effects in fungal...
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... species. This PhD project deals with the bioinformatics analysis of RNA-Seq data in order to identify AS events in human-pathogenic fungi and to predict the effect of AS on the infection process. Therefore, different tools for mapping of RNA-Seq data and detecting significantly alternatively spliced genes are used. A workflow for the reliable prediction of AS events in fungi will be developed. Identified AS events are the basis for multi-species comparisons which will gain new insights into the evolutionary connection of AS in fungi. Furthermore, it is of interest to discover the consequences of AS concerning their protein structure.
 
 
Siscar, Sofia Lewin

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JSMC Fellow

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

Host adaptation, avirulence and antivirulence genes of Candida glabrata

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Abstract: Microbial evolution and adaptation to specific niches, such as the human body, are driven by genetic mutations and alterations including gain of new genes, modification of existing...
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... genes, but also loss of genes detrimental for survival in a particular niche or for a particular life style. For example, Yersinia pestis, a highly pathogenic micro-organism, has lost multiple genes and has a smaller genome than less pathogenic species; and M. leprae, the causative agent of leprosy, shows an extreme gene reduction concomitant with a loss of many metabolic functions. Candida glabrata is a commensal member of the microbiome in the majority of humans. However, it is also common opportunistic pathogen causing superficial to life-threatening infections under certain predisposing conditions. Of note, C. glabrata is phylogenetically more closely related to the baker’s yeast Saccharomyces cerevisiae than to other important pathogens such as C. albicans, and has developed pathogenicity strategies during host adaptation which differ markedly from the latter. One remarkable attribute of C. glabrata, in contrast to C. albicans, is the loss of distinct metabolic pathways resulting in several auxotrophies, which allow fungal cells to sense these molecules in the host to initiate a response suitable for fitness, survival and infection. Another example for genetic loss are secreted proteins of C. albicans, which elicit immune response in the host. C. glabrata, in contrast, lacks many of these proteins, and hence immunogenic signals and in general elicits a much lower immune response in ex vivo and in vivo models. Since C. glabrata has evolved pathogenicity mechanisms as an opportunistic pathogen, which is phylogenetically closely related to the baker’s yeast Saccharomyces cerevisiae, we aim to elucidate which particular genes of C. glabrata have diverged (possible avirulence genes, which would elicit a host response in the original form) or have been lost (potential antivirulence genes, which would reduce pathogenesis by their function) during host adaptation. This will increase our understanding of the past evolution of metabolism and interspecies molecular signaling between pathogens and their host. Characterizing these avirulence and antivirulence genes may help to identify new biomarkers and potential targets for antimycotic drug development. Importantly, the selection of the genes to be investigated in this project will be based on in silico analyses of existing transcriptional profiles, which have been obtained during simulated ex vivo infection of a whole-blood model. Additionally, this selection will also be based on in silico analysis of the evolution of C. glabrata and its related species, in cooperation with international collaboration partners.
 
 
Sporniak, Marta

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JSMC Fellow

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

Towards therapeutic microbes: Synthetic antifungal bacteria

 
 
Sreekantapuram, Venkata Naga Sravya

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Institute/Dep.
 
 
Stanford, Felicia

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JSMC Fellow

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute and Friedrich Schiller University Jena
Jena Microbial Resource Collection (JMRC)
PhD Project:

Adaptive traits as mediators of stress response and virulence in Lichtheimia

 
 
Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Dept. Molecular and Applied Microbiology
Friedrich Schiller University Jena
Institute for Materials Science and Technology (IMT)
PhD Project:

Antimicrobial Effect of Nano-Rough Titanium Surfaces: Reduction of Microbial Adhesion and Mechanisms of Reduction

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

Application of Orbitrap-GC/MS to metabolomics research