Scope of Research Themes

Upon being accepted into the PhD programme students will become acquainted with the research themes that can be adopted for their PhD work. These themes are integrated into the scope of the research done by the participating research laboratories. Some examples are:

Cristina Timóteo / UCIBIO, FCT, UNL, Portugal

The group aims at understanding the mechanism of functioning of oxidative stress sensors in pathogenic bacteria:

1. Desulfovibrio vulgaris PerR. This bacterial repressor has a structural metal center with zinc and an active site containing iron. In the presence of these two metals and hydrogen peroxide it adopts an open conformation unable to bind to DNA, allowing the expression of oxidative stress protection enzymes, such as catalase or bacterioferritins. 

2. Staphylococcus aureus AirSR. AirSR is a [2Fe-2S] containing two-component system (TCS) recently isolated from S. aureus. TCS frequently control the expression of virulence genes in pathogenic bacteria. AirS subunit is a kinase, that catalyses the autophosphorylation of a histidine residue, and subsquently transfers the phosphoryl group to an aspartate residue of AirR. AirS's kinase activity was inactivated by strong oxidants such as NO and H2O2, or prolonged exposure to oxygen.

To achieve our aims several methods are used:

Recombinant DNA techniques: cloning, recombinant heterologous protein expression, site-directed mutagenesis.

Rapid kinetics methodologies: UV/Visible and fluorescence stopped-flow, EPR and Mössbauer spectroscopies coupled to Rapid Freeze-Quench.

DNA-protein interactions. EMSA.


Stephan Denifl / University of Innsbruck, Austria 

Our group investigates low energy electron induced processes in various biomolecular systems by means of experimental methods. Low energy electrons are the most abundant secondary species formed by ionizing radiation in biological matter and important for the chemical transformation of biomolecules. 

To give a short general overview, we apply mass spectrometric methods, where we generate a low energy electron beam, cross this beam with a biomolecular target beam and detect the charged reaction products with a mass spectrometer. The biomolecular systems studied range from small molecular building blocks up to nanosized species. Our experiments allow to study physical/chemical aspects of radiation damage, which are happening before the biological time scale. 

Due to this line of research a previous education in physics or chemistry (MSc, in physics or chemistry) is beneficial for a research stay in Innsbruck, particularly if a possible enrollment in the physics PhD-study at the University of Innsbruck is intended. 

If you are interested to carry out a PhD within the RaBBit-programme or for further questions, please contact me by e-mail: Stephan.Denifl@uibk.ac.at

 

Gustavo García / Spanish National Research Council (CSIC), Spain

Radiation-matter interactions (RMI)

Radiation sources: Electron and ion sources. Photon sources. . Radioactive sources Atomic and molecular beam generation. Sources producing neutral and charged radicals.

Interactions of charged particle with matter: Atomic and molecular collision cross section determination (experiments and theory). Elastic and inelastic processes. Bremsstrahlung. Positron annihilation. Energy deposition and stopping powers.

Photon interactions with matter: Photoionising processes (photoelectric and Compton scattering). Rayleigh scattering. Pair creation.  Atomic and molecular excitation.

Particle accelerators. Particle detectors and spectrometers. Basic principles and apparatus design. Signal analysis end related electronics.

Modelling particle transport in matter. Boltzmann equation and Monte Carlo methods.

 

Jimena Gorfinkiel / The Open University, UK

Understanding electron induced break-up (theory).

Investigation of electron initiated break-up of molecules of biological importance and how the environment (solvation) affects the processes.

Using sophisticated ab initio techniques  to study low energy electron attachment and how it leads to molecular damage. Understanding this processes is crucial to fully understand radiation induced damage in biological (and other) media.  Work involves running and developing software and methodology, gaining knowledge and expertise in molecular physics, quantum chemistry and software development.

Suitable for students with a good Physics or Chemistry (theoretical/computation) degree.

 

Nigel Mason / The Open University, UK

Electron interactions with biomolecules; dissociative electron attachment to biomolecules; experimental studies of DNA damage; Spectroscopy of biomolecules using synchrotron radiation; role of nanoparticles in cancer therapy;

Plasma interactions with biomolecules and plasma sterilisation.