Doctoral Researchers

 
Saraiva, João

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JSMC Fellow

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Network Modeling
PhD Project:

Exploring unbound human and mouse inflammatory defense mechanisms against bacterial and fungal infection employing bioinformatics/systems biology concepts

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Abstract: Systemic infection of the human host can arise from pathogenic bacteria such as Staphylococcus aureus and non-pathogenic bacteria such a E. coli, but also from overall abundant fungal...
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... species such as Candida albicans. Such infections can lead to an unbound inflammatory response of the human host and finally sepsis. Sepsis is one of the leading causes of death world wide. Besides this, the Systemic Inflammatory Response Syndrome (SIRS) can arise from injury without an infectional cause. SIRS comes also along with unbound inflammation. It has similar clinical symptoms at time of diagnosis but the patients show a much better recovery in comparison to sepsis. Inflammation caused by fungi and bacteria seem to utilize different signaling pathways. The aim of the project is to - explore signaling and metabolic networks in the immune cells to enroll similarities and differences between these diseases (bacterial and fungal caused inflammation, SIRS), - put up mathematical models for the different causes of inflammation (fungal, bacterial, SIRS) which explain the different regulatory response, and to use these models i) for predicting the cause of the disease, ii) to elucidate the difference in cellular regulation between the different microbial and non-microbial caused dis-regulations and to get an insight into the communication between immune cells and the parasitic microbes, and iii) to identify targets for switching back the immune cells from a pathogenic back to a normal like behavior, i.e from unbound to controlled inflammation.
 
 
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.
 
 
Schaeme, Daniel

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ChemBioSys Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute of General Botany and Plant Physiology
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

 
 
Schmalwasser, Andreas

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IMPRS Student

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Geosciences
Chair for Hydrogeology
PhD Project:

MOPS in the critical zone – the neglected mobile pool of soil organic matter

 
 
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

 
 
Schoeler, Hanno

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FungiNet 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:

Imaging und Proteomanalyse der Interaktion von Aspergillus fumigatus mit Neutrophilen Granulozyten

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Abstract: Aspergillus fumigatus is the most important air-borne human-pathogenic fungus. This opportunistic pathogen can cause invasive aspergillosis in immunosuppressed patients (e.g. organ...
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... recipients or patients with CGD). The PhD-project aimes to analyse the interaction between the neutrophil granulocytes and the fungus. It is on the one hand of interest to highlight the role of the DNases that are secreted by the fungus. On the other hand the project should elucidate the host defense-strategies upon confrontation with Aspergillus fumigatus, especially the formation of neutrophil extracellular traps (NETs) - DNA-fibers suspected to inhibit fungal growth and to mark it for the immune system. The latter process could serve for recognition of the fungus by the immune cells which will be investigated with a confocal laser-scanning microscope. Within an interdisciplinary framework the time-laps movies will then be analysed in-silico by the bioinformatic department of the HKI. In another collaboration with the Universitätsklinikum Würzburg an analysis of differences in NET-formation is planned. Here, the influence of selected genetic diseases, resulting in impaired neutrophil activity, will be investigated in more detail. Previously, the transcriptome of neutrophil granulocytes was studied. For this project the next step will be performed by generating the proteomic map of the neutrophil granulocytes during infection. The project highlights the interactions between neutrophil Granulocytes and the human-pathogenic fungus Aspergillus fumigatus. This includes also all kinds of communication between them. There are distinct signs for the immune system that a pathogen is present which lead to subsequent activation of the immune reaction, for example the NET formation. But there are also signals for the pathogen about the hostile environment it is colonizing which leads to avoidance strategies. Therefore, investigation of the complex interplay between the host and the fungus will not only contribute to the understanding of infection by Aspergillus fumigatus but might also serve as a model for immune defense mechanisms towards other fungal pathogens.
 
 
Schulze, Sylvie

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FungiNet Student

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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:

Systems based modelling of human fungal pathogens interacting with the human immune system

 
 
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

 
 
Sester, Angela

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ILRS Student

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute-
Junior Research Group
Secondary Metabolism of Predatory Bacteria
 
 
Shitut, Shraddha

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IMPRS Student

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

Unraveling the dynamics of metabolite production in cross-feeding populations and study its effect on the interactions

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Abstract: No organism exists in isolation in nature. There are numerous interactions taking place; some of which entail exchange of information between microbes. This information has been shown...
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... to be of different types like DNA, metabolites, toxins and so on. My work focuses on the exchange of metabolites between synthetically engineered strains of Escherichia coli and Acinetobacter baylyi. The metabolite being a nutrient (amino acid) also affects the physiology of the partners. Availability of this nutrient in the surrounding could alter internal levels and subsequently the interaction between the partners. Understanding how this exchange is regulated gives an insight of how organisms interact in a community. A major part of the interaction is not only the process but also its result. These interactions in-turn shape the community and also the physiology of the organisms. Another aspect of the study will be to study the interaction between partners with a perspective of experimental evolution. This also throws light on its frequent occurrence in nature.
 
 
Shopova, Iordana

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FungiNet 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:

Communication between human polymorphonuclear granulocytes and Aspergillus fumigatus

 
 
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.
 
 
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

 
 
Sumanovac Sestak, Ivana

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JSMC Fellow

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Institute/Dep.
Leibniz Institute of Photonic Technology (IPHT)
Dep. of Microscopy
Leibniz Institute for Age Research, Fritz Lipman Institute (FLI)
Dep. Molecular Biology
PhD Project:

Developing a palm-compliant MELC process for the structure elucidation of the human kinetochore

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Abstract: The PhD student will develop a novel mode of microscopy imaging which aims at obtaining structural biological information at a resolution down to about 30nm for many (10-100) target...
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... molecules associated with the kinetochore complex. The methodology is based on combining a high resolution single molecule technique (photo activated localization microscopy, PALM) and addressing the multiple molecular targets by using multi-epitope ligand cartography (MELC). Both of these techniques have been shown to achieve impressive results and thus the combination should be capable of producing extremely valuable scientific information about the organisation of the kinetochore. The three-dimensional molecular structure of the kinetochore is still unknown but is essential for the understanding of its function and its role in cancer development. This project is situated within two highly motivated groups in the interface between Biology (Prof. Stephan Diekmann, Kinetochore complex) and Physics (Prof. Rainer Heintzmann, high resolution microscopy techniques), where experience, team-work and guidance with many aspects of the project will be provided.
 
 
Sundaram, Srividhya

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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. Biomolecular Chemistry
PhD Project:

Elucidation of Complex Biosynthetic Pathways in Microorganisms