This is the list of our available 14 PhD Projects for 2015. You can only apply for these 14 projects.
During the online application process, you will be asked to choose three favourite projects in the order of preference.
Please check out all projects in detail.
Seed number is a genetically determined trait that is variable and strongly modified by the environment. This project will analyse in detail how small secreted peptides and their corresponding receptors trigger signaling pathways control seed number in the model plant Arabidopsis, and how environmental factors such as growth temperature alter the activities of these pathways. The knowledge gained here will be used to modify this important trait in a crop plant, such as rapeseed.
Group: Rüdiger Simon (HHU)
HHU_B: Genotype-Phenotype Map for Molecular Modules in Arabidopsis Thaliana
This computational biology project tries to establish a genotype-phenotype map of molecular complexes using probabilistic causal networks. The causal networks are constructed from direct correlations between nucleotides and amino acids, which are inferred from sequence data. As data source we will use the catalog of Arabidopsis Thaliana genetic variation, which currently comprises more than 1100 lines.
Group: Markus Kollmann (HHU)
HHU_C: C3-C4 intermediate species as models for early evolutionary steps on the path to C4 photosynthesis
C3-C4 intermediate plant species display lowered CO2 compensation points in comparison to C3 species. This is due to the operation of a primitive CO2 concentrating pump, which is based on a shift of photorespiratory GDC activity from leaf mesophyll to bundle sheath cells. C3-C4 intermediate species are therefore considered as naturally occurring evolutionary intermediates on the path from C3 to C4 photosynthesis. This project aims at identifying the key players of these first steps of C4 evolution by correlation of genetic, phenotypic, and physiological traits in a segregating mapping population of hybrids between C3 and C3-C4 intermediate Moricandia species (Brassicaceae).
Group: Andreas Weber (HHU)
UoC_A: Identification of genes regulating life history traits and study of their evolutionary significance between annual and perennial plants
This project aims to identify and characterize genes involved in life strategy evolution between the perennial Arabis alpina and the annual Arabidopsis thaliana. A. alpina mutants available in our laboratory will be characterized and causal mutations will be cloned by whole genome resequencing. To understand the involvement of identified genes in the annual and perennial life cycle comparative studies will be performed between A. alpina and A. thaliana.
Group: Maria Albani (UoC/MPIPZ)
UoC_B: Genome-scale transcriptional regulatory networks involved in the plant response to phosphate availability and interactions with soil fungi
Phosphate starvation stress strongly affects plant-microbe interactions but the mechanistic basis of these interactions is hardly understood. In this project the participating PhD student will learn diverse methods, both theoretical and practical, and will build a model on how plants integrate environmental factors into their response to biotic interactions in close interaction with the co-operating partners (molecular plant physiology, plant biochemistry, bioinformatics, quantitative biology). The results are expected to reveal novel regulatory circuits in the control of plant growth and plant-microflora interactions by phosphate. Data sets from transcriptome experiments will be combined into a large meta-analysis to increase the statistical power of predictions and will be used to infer gene regulatory relationships in the response of plants to abiotic factors such as phosphate starvation, and in plant symbiosis with beneficial fungi. Candidate regulatory genes will subsequently be validated in Arabidopsis accessions widely differing in phosphate content, and in mycorrhizal Lotus japonicus and non-mycorrhizal Arabidopsis mutants colonized with soil-based fungi.
Groups: Marcel Bucher and Stan Kopriva (UoC)
UoC_C: Genomic basis of Arabis nemorensis ecological adaptation to the Rhine floodplains
Our contemporary societies are marked by rapid habitat degradation. Restoring an environment after its destruction is a difficult task. In this context, understanding the population genetics and history of key species in endangered ecosystems has become crucial. This project will investigate the population genomics of Arabis nemorensis, a key species in species-rich floodplain meadows, which form a shrinking yet ecologically unique habitat. An analysis of polymorphism and divergence throughout the genome will highlight genes targeted by natural selection in this species with singular ecology.
Group: Juliette de Meaux (UoC)
The plant hormone jasmonate promotes the terminal stages of stamen development, including filament elongation and anther dehiscence, which result in anthers correctly positioned close to pistils and in pollen release. We are currently establishing barley as a model system to study these processes in cereals. The goal of this project is to identify and characterize factors necessary for barley jasmonate signaling, filament elongation and anther dehiscence. The project will use a combination of genetics, genomics, histology and bioimaging to achieve this goal.
Group: Ivan F. Acosta (MPIPZ)
MPI_B: Understanding the cis-regulatory code of chromatin-mediated repression in plants
The evolutionary conserved Polycomb Group (PcG) pathway provides a mechanism for gene repression by chromatin compaction. We have recently identified a cis-regulatory element that is correlated to PcG target genes in Arabidopsis thaliana. The aim of the proposed project is to establish the role of the candidate cis-element in PcG target gene regulation in higher plants. The ideal candidate for this project is a molecular biologist with a strong motivation to learn basic scripting and command line tools to perform bioinformatics analysis.
Group: Franziska Turck (MPIPZ)
MPI_C: An evolutionary framework for plant environmental stress signaling
Mechanisms for coping with contrasting biotic and abiotic stresses in the environment are fundamental for plant survival and adaptation. In this project we will use protein phylogenetic and structural data on a plant disease resistance signaling node to investigate the extent of its evolutionary conservation between a dicot species, Arabidopsis, and a monocot crop, barley (Hordeum vulgare). In Arabidopsis, the resistance node controls transcriptional decision making between different stress hormone pathways. We will explore whether the same transcriptional functions are maintained in barley.
Group: Jane Parker (MPIPZ) and Maria von Korff (HHU/MPIPZ)
MPI_D: In planta bacterial transcriptome analysis in Arabidopsis thaliana and its relatives
Despite accumulated knowledge about plant immune responses triggered by recognition of bacterial pathogens, very little is known about how plants suppress bacterial growth. In this project, we will tackle this major remaining question by analyzing in planta bacterial transcriptome and proteome in Arabidopsis thaliana and its relatives using RNA-seq and quantitative proteomics. In planta bacterial profiles will provide fundamental insights into our understanding of bacterial growth suppression mechanisms by plant immunity. During the course of the study, the PhD student will gain a broad range of state-of-art skills in genetics, molecular biology, and bioinformatics.
Group: Kenichi Tsuda (MPIPZ)
MPI_E: The role of mechanical signals in shaping the Arabidopsis sepal
Recent studies suggest that plant cells can sense forces, and respond to stress by reorienting microtubules, which in turn direct cellulose synthase complexes. This suggests that stress may play a signaling role in morphogensis by influencing cell wall anisotropy and growth. The Arabidopsis sepal is an easily accessible organ that is remarkably uniform in shape, although it has very large variability in shape at the cellular level. Since cell shape can greatly affect stresses in the cell wall, the sepal provides an excellent system to explore the role of mechanical signals in morphogenesis. In this project we will perform mechanical measurements on the sepal using osmotic treatments and the Cellular Force Microscopy system that has recently been developed in the Smith lab. Combined with high resolution growth tracking using MorphoGraphX (www.MorphoGraphX.org), we aim to understand the role of mechanical signaling in guiding sepal shape.
Group: Richard S. Smith (MPIPZ)
MPI_F: Genome-wide association studies to define components and mechanisms underlying an evolutionarily conserved NLR-mediated immune response
Intracellular nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) are key components of the innate immune system of plants. This proposal aims to unravel an evolutionarily conserved 1) recognition mechanism for pathogen effectors involving allelic MLA receptors and 2) MLA immune signaling using genome-wide association studies with isolates of the powdery mildew fungus Blumeria graminis f. sp. hordei (Bgh) and ecotypes of Arabidopsis thaliana, respectively. The former project will also provide insights into the evolutionary history of pathogen effectors in response to the host immune surveillance.
Group: Paul Schulze-Lefert (MPIPZ) and Takaki Maekawa
MPI_G: The role of cell geometry and anisotropy in explosive pod shatter
The aim of this project is to identify the mechanics and genetics underpinning developmental changes in cell shape and anisotropy that drive explosive pod shatter in Cardamine hirsuta. This plant stores elastic energy in its fruit tissues before rapidly transforming it into kinetic energy to ballistically disperse its seeds. In this project, we will identify key genetic components of the energy storage mechanism in C. hirsuta fruit.
Group: Angela Hay (MPIPZ)
MPI_H: Identification of target genes of the Reduced Complexity (RCO) transcription factor
Leaves present an iconic and prevalent example of biodiversity as they are abundant in the biosphere and show striking variation in shape. However, it is not clear how such diversity is generated. Leaf form can be classified as simple, where the leaf blade is entire like in the model plant A. thaliana, or dissected (compound) where the blade is divided into leaflets. In the past few years we have made key contributions to understanding the genetic pathways underlying leaf shape diversity by developing the A. thaliana relative C. hirsuta into a powerful experimental system to study diversification of leaf form in an unbiased fashion. We leverage the simple genetics and transformation in both species to understand the mechanistic basis for leaf shape evolution. Recently we discovered the RCO gene which encodes a homeodomain protein required for leaflet formation (Vlad et al., 2014). We also showed that RCO evolved in the Brassicaceae family through gene duplication and was lost in A. thaliana, contributing to leaf simplification in this species. Thus RCO provided a rare example of gene whose presence or absence in the genome of two closely related species is sufficient to explain a large component of their morphological diversity. To understand how RCO exerts its effects on leaf development we propose to isolate RCO target genes and study their functions.
Group: Miltos Tsiantis (MPIPZ)