Doctoral Researchers

 
Gallegos Monterrosa, Ramses

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Institute/Dep.
Friedrich Schiller University Jena
Institute of Microbiology
Junior Research Group Terrestrial Biofilms
PhD Project:

Cell-cell communication in single species and mixed biofilms

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Abstract: Background Biofilm formation costs and benefits the society. On one hand biofilms can be negative, for example, biofilms are a source of contamination in food processing equipment,...
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... can reduce heat transfer in cooling towers, increase drag on ships, foul reverse osmosis membranes and even corrode metal surfaces; moreover, since biofilms have great resistance to antimicrobial treatment, they are difficult to control in industry or the clinic. On the other hand, biofilms can be also beneficial, such as in the case of biofilm formation by Bacillus subtilis in various crop plant root systems. In most cases biofilm formation has been targeted (to prevent or to promote) by altering the ability of bacteria to attach itself to surfaces or by changing pathways involved in matrix production. Aim The current project is involved in the cell-cell communication (i.e. quorum sensing) in single- and multi-species biofilms. The role of various B. subtilis produced quorum sensing molecules will be examined during biofilm formation. Further, the role of various global transcription regulators will be examined in a novel approach based on random mutagenesis to identify the important features of these regulators during biofilm development and in quorum sensing. Finally, the current project aims to get a better insight into quorum sensing through the use of mixed species biofilms and reveal the effect that different Bacillus species may have over the development of B. subtilis biofilms. The different parts of this project will all aim to characterize and identify possible targeting of quorum sensing in bacterial biofilms that could be further exploited in medical or biotechnological settings.
 
 
Garbe, Enrico

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Institute/Dep.
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI)
Junior Research Group Host Fungal Interfaces
PhD Project:

Transcriptional control of environmental pH modulation in the fungal pathogen Candida albicans

 
 
Garrone, Alessio

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JSMC Fellow

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Institute/Dep.
Leibniz Institute of Photonic Technology (IPHT)
Dep. Spectroscopy/Imaging
Friedrich Schiller University Jena
Institute of Physical Chemistry
PhD Project:

Photoreaction of the NADPH-Protocholorophyllide-Oxidoreductase from Synechocystis – The Ultrafast Mechanism of Adapting a Metabolic Pathway to an Environmental Stimulus

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Abstract: Microbes - as any living organism - need to adjust their metabolism to a multitude of external stimuli a prominent one being the exposure to light, upon which biochemical pathways are...
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... regulated. The primary mechanistic step of the response is typically the photoinduced alteration of molecular structures in a photoactive protein such as rhodopsins or phytochromes. Nonetheless, there also exist two enzymes, which require the absorption of light for the catalytic function. Thereby their function can be directly triggered by the exposure to light. One of these two enzymes is the NADPH:protochlorophyllide?oxidoreductase (POR), which is known from cyanobacteria and higher plants. POR plays a central role in the light regulation of the chlorophyll synthesis. It catalyzes one of the later steps in the chlorophyll synthesis pathway: the light?dependent reduction of protochlorophyllide (PChlide) to chlorophyllide by trans addition of hydrogen across the C17?C18 double bond in the porphyrin ring. Because POR is activated by light it can provide information on the way in which light energy is used to control the enzymatic activity of living organisms in general. Within this project the mechanistic interplay between protein structure and enzyme function will be investigated on an ultrafast timescale (on the time scale of picoseconds, i.e., 10-12 s). This is done by combining mutagenesis studies of the catalytic reaction center with various spectroscopic tools such as femtosecond time-resolved differential absorption (in the UV/Vis and mid-IR spectral range) and picosecond time-resolved luminescence measurements. This combination of techniques enables the assessment of individual protein sites, which are critical for the ultrafast photoresponse of the enzyme, and the determination of the relevant reaction coordinates on an ultrafast time-scale. This is of particular interest as it has been shown previously that processes on a sub?picosecond/ picoseconds timescale determine the overall efficiency of a photodriven reaction. Additionally, comparative studies on the ultrafast reactions of PORs from photosynthetic eucaryotes will be pursued in this project in order to address the question of whether the catalytic mechanism of the light-dependent PORs has evolved from the cyanobacterial enzyme.
 
 
Gore, Sagar

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ChemBioSys 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:

Pattern recognition methods for prediction of chemical structure of fungal secondary metabolites

 
 
Gusewski, Sandra

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ILRS Student

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Institute/Dep.
Friedrich Schiller University Jena
Chair of Genetics
PhD Project:

Assessing DNA-binding specificity of MADS-domain transcription factors

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Abstract: The specific molecular interaction between DNA and transcription factors (TFs) is of utmost importance to control gene expression and thereby cell differentiation and organ development....
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... Consensus sequences for DNA-binding sites have been defined for many TFs. However, more elaborate principles are still lacking that define which features turn a certain DNA sequence, which might exist in several thousand copies in the genome, into a true recognition site. It will be studied to which extent the primary DNA sequence (“base readout”) and also the sequence-dependent shape of the DNA (“shape readout”) contribute to binding specificity of a TF. To address this issue, MADS-domain proteins will be used as a model system. They are found in almost all eukaryotes, but have especially prominent developmental functions in seed plants. SEPALLATA3 (SEP3), a MADS-domain transcription factor involved in flower development, will serve as a starting point of research since this factor has already elicited considerable scientific interest. Within this project, the thermodynamics and kinetics of the molecular interactions of SEP3 with DNA will be studied, using a variety of biophysical, bioinformatics and molecular biology tools. The structural characteristics of the protein, the DNA and the protein-DNA-complexes will be determined using circular dichroism (CD) spectroscopy. Bioinformatic sequence analyses will reveal candidate amino acid residues that may be involved in determining binding specificity. Based on these results, proteins with amino acid substitutions will be generated to gain additional insights into how different residues contribute to binding specificity.