Bachelor and Master Projects

Interested students who wish to perform a project in the group are invited to Prof. Nynke Dekker to learn about more detailed aspects of the group, the expectations we have of students, and the timeframe.

A general overview is given below:

  • Students are fully integrated in our multidisciplinary team, gaining a unique experience at the frontier of research
  • The projects include all aspects of practical lab work, experiments and analysis
  • Every student will grow in his or her skills and become independent to a level where he or she can make a real contribution to research at the cutting edge of science, often including a publication in an international scientific journal.

The laboratory is currently (Jan 2017) quite full with students, as a result of which we do not have any Bachelors projects available until the summer. For Masters students we have the following student projects available:

1. DNA Transcription: Function of RNA Polymerase Transcription Factors

RNA polymerases (RNAP) are a main target for the regulation of gene expression and thus a possible target for antibiotics and vaccines. RNAP are highly conserved across different organisms And the RNA chain elongation is   stochastic and highly dynamic, interrupted by pauses that represent a gene regulatory feature; they facilitate the timely interaction of regulatory factors and the synchronization with the subsequent translation. We characterize the transcription mechanism and related pausing events during RNA chain elongation of E. coli RNA polymerase on a single-molecule level as model system. The RNAP dynamics are probed under different experimental conditions, e.g. we study the force and nucleotide concentration dependencies, as well as the effects of the nucleotide analogue inosine to the proofreading mechanism, and the role and impact of the most important transcription elongation factors that are expressed in the cell.

RNA chain creation by RNA polymeraseRNA chain creation by RNA polymerase

1.1 Detailed BEP/MEP project description

Students will be involved in projects creating a mechanistic kinetic model of the regulation of gene expression and determine further the impact of transcription factors. The selected transcription factors correspond to fundamental mechanisms such as proofreading, recuperation from arrested states, DNA-repair process, virulence and anti-termination.
• Studying the impact of the virulence factor RfaH to the transcription process. RfaH is considered as major target for novel antibiotics. .
• Characterize the influence of RNA cleavage factors and DNA repair factors on RNAP dynamics and processivity.
• Probing the transcription dynamics under macromolecular crowding conditions, simulating as such the cellular environment.

Contact
Dr. Richard Janissen
Dept. of Bionanoscience, TU Delft
Room F090, Tel: +31-152783552
Email: R.Janissen@tudelft.nl