Friedrich-Schiller-Universität Jena

Topics for bachelor and master theses

Project I

Protein-DNA interactions of MADS-domain proteins

Info: Florian Rümpler

The flower development of angiosperms is controlled by floral homeotic MADS-domain transcription factors that act in a combinatorial manner to control the development of all four types of floral organs (sepals, petals, stamens and carpels). The combinatorial activity relies on highly specific protein-protein interactions that allow for the formation of DNA-bound, floral organ specific tetrameric complexes (floral quartets). Recent studies have indicated that the protein-protein interaction network of MADS-domain proteins changed during early angiosperm evolution and that these changes probably contributed to the canalization of flower development. In this project the protein-protein interaction capabilities of MADS-domain protein representatives from different angiosperm species will be analyzed in vitro to comprehend the evolutionary trajectories that allowed for the development of a clearly structured floral bauplan with functionally and structurally highly specialized floral organs.

Wet-lab methods: molecular cloning, site directed mutagenesis, SDS-PAGE, EMSA

Bioinformatical methods: phylogeny and ancestral character state reconstruction, selection analysis



Project II

Molecular Evolution

Info: Lydia Gramzow;

With experimental part

1. Identification of miRNAs targeting MADS-box genes

a. miRNAs targeting AGL17-like genes in plants other than Arabidopsis thaliana and Oryza sativa

  • Methods: Identification of AGL17-like genes in the corresponding genomes, phylogenies; Identification of miRNA candidates using prediction programs; Experimental verification of expression of miRNA candidates

b. miRNAs targeting MADS-box genes other than AGL17-like genes in Arabidopsis thaliana and Oryza sativa

  • Methods: Identification of miRNA candidates using prediction programs; Experimental verification of expression of miRNA candidates

2. Phylogeny and selection analyses of genes homologous to LFY and AG in gymnosperms

  • Methods: Isolation of gene sequences from the corresponding plant species; Phylogeny estimation; Selection analyses

Without experimental part

3. Phylogenomics of MADS-box genes in plants

  • Methods: Identification of MADS-box genes in whole plant genomes using Hidden-Markov-Model Searches; Annotation of genes, identification of corresponding EST-sequences; Phylogenies; Characterization of types, groups and clades of MADS-box genes

4. Origin of the keratin-like domain

  • Methods: Identification of sequences with remote homology to the keratin-like domain; Model of the evolution of the keratin-like domain and its association with the MADS domai



Project III

Analysis of CRISPR/Cas9-induced mutants

Info: Andrea Hoffmeier

To better understand the evolutionary significance of homeotic mutants we are studying a floral homeotic variety of Capsella bursa-pastoris (shepherd's purse) in which all petals are transformed into stamens. We identified the AGAMOUS gene encoding a transcription factor as the likely candidate gene responsible for the mutant phenotype.

Using CRISPR/Cas9 technology, we want to confirm the transcription factor as the cause for the mutant phenotype. In consultation with the potential applicant various techniques will be applied to analyse the obtained mutants, such as PCR-analysis, microscopy, expression analysis using real-time PCR, Southern blot, cloning and further plant transformations with the CRISPR/Cas9 system. 

The information can be downloaded here.