Project Proposals for IMPRS 2014
Directions in coevolution between plant and microbes: Who decides?
Under natural conditions, plants are part of an interaction network including a broad range of symbiotic microorganisms ranging from mutualists to pathogens. Obligate plant colonizers that rely on a living host to survive, can live endophytic - symptomless, or pathogenic, harming their host. Goal of this project is to develop a dynamic coevolutionary network based on high throughput amplicon and genome sequencing of time course samples to determine evolutionary triggers leading to a switch in relationships between plants and microbes and therefore to a change in direction of coevolution.
Computational and genetic analysis of genomic variation in perennial Arabis alpina
We have developed the sister species Arabis alpina and Arabis montbretiana as a model system for studying evolution of annual from perennial life history. Annuals characteristically live for one year, die after flowering and produce high seed yields, whereas perennials live for many years but produce fewer seeds each year. We have sequenced the genomes of both model species. This project will compare the resequenced genomes of accessions of perennial Arabis alpina collected in different geographical locations and analyze these together with the data from genetic experiments based on crossing such plants to identify genes associated with adaptation of perennials to different environments. Particular focus will be given to accessions varying in flowering and reproductive traits.
Phylogeny and function of Polycomb Group gene family expansion in Brassicaceae
Polycomb Group (PcG) protein complexes play an essential and universally conserved role in epigenetic gene repression supporting the proper development of multicellular organisms across all kingdoms. In higher plants, the genes encoding for several PcG proteins have expanded. The aim of the IMPRS PhD project is to characterize isoforms generated after gene expansion to elucidate the effect and thus reason for gene family diversification. This will be achieved by performing extensive domain swap experiments in transgenic plants and by establishing an assay to measure the catalytic activity of PcG protein complexes in vitro. A particular focus will be the comparative analysis of PcG proteins encoded by Brassicaceae species showing a different count of family members.
The function of Lateral suppressor in root development
The aim of the proposed project is to characterise the function of the LATERAL SUPPRESSOR (LAS) gene during Arabidopsis root development in comparison with its function during axillary meristem formation in the shoot. This study will include an analysis of LAS expression in the root, the identification and a characterisation LAS target genes and their interactions with known regulators of root development. Furthermore, the evolutionary conservation of selected target genes will be studied.
Paul Schulze-Lefert, together with Marcel Bucher:
Dissecting a multitrophic interaction network at the plant root-soil interface
Fungal and bacterial communities coexist in soil and functionally interact in the rhizosphere, forming mixed consortia that have central roles for plant health and productivity. By combining deep microflora community profiling, microbial cultivation and functional studies, we aim (1) to understand how complex multitrophic and inter-kingdom root-associated microbial communities are taxonomically organized and interact functionally and (2) to assemble synthetic microbial communities that have synergistic beneficial impact on plant growth and health.
Evolutionary conservation and diversification of immune networks in Arabidopsis thaliana and its relatives
Analysis of plant immune networks has been dependent on limited species. Consequently, we lack comprehensive understanding of evolutionary conservation and diversification of plant immune networks. In this project, we will characterize immune responses and network behaviors in Arabidopsis thaliana and its relatives using molecular genetics, genomics and computational approaches. This study will reveal functional core components and structures as well as evolutionary diversification of plant immune networks.
Miltos Tsiantis, together with Richard Smith:
An interdisciplinary approach to understanding leaf development and diversity.
A key challenge in biology is to understand how diversity in organismal form is generated. We developed Cardamine hirsuta - a relative of the model plant Arabidopsis thaliana - into a versatile system for studying morphological evolution. Here we aim to understand the morphogenetic paths leading to the strikingly different geometries of the two species: simple leaves in A. thaliana and dissected leaves with leaflets in C. hirsuta. To achieve this we will use a combination of genetics, advanced imaging and computational modeling. Further we will investigate to what degree principles we derive from studying the divergent leaf forms of A. thaliana and Cardamine are sufficient to explain the large variety of leaf shapes seen in seed plants. The project will be instrumental in producing predictive models of a leaf shape, a trait that evolves in close correspondence with the environment suggesting it may be of adaptive significance.
Richard S. Smith, together with Achim Tresch
Cell lineage tracking and growth analysis by 4D meshes generated from confocal images
The goal of the project is to automatically track cell division and growth of leaves using 3D time lapse data from confocal images. Our approach will be to extract the surface of the sample into a mesh (graph), project an image of the cells on this mesh, and then adapt algorithms for 2D and 3D image processing to work on graphs. We will then apply graph alignment algorithms on cell networks obtained from segmentation of successive time points. The result will be a complete lineage map of development at the cellular level.
Metabolic interdependencies in plant-endophyte interactions
The project aims to identify secondary metabolites which affect root colonisation by endophytic microorganism observed in two Arabidopsis thaliana mutants defective in the production of specific secondary metabolites. This approach will improve the understanding of mechanisms by which plants shape their microbiome.
Genome-scale transcriptional and metabolic regulatory networks involved in the plant response to phosphate starvation stress
Phosphate starvation stress affects plant architecture, metabolism, hormone balance and plant-microbe interactions. In this project, bioinformatics analysis of already available whole genome large scale RNA sequencing and metabolite profiling experiments will be used to predict the core regulatory system controlling activation and repression responses to phosphate starvation in different plant species. Network and flux balance analysis will reveal candidate genes and metabolites which can subsequently be validated in functional genomics and molecular physiological experiments.
The evolution of light signaling: Analysis of light responses and the role of COP1/SPA activity on transcription factors in Physcomitrella patens
Light signaling in Arabidopsis is well understood and involves photoreceptors, an E3 ubiquitin ligase and transcription factors that are targeted for degradation in darkness. However, little is known about the evolution of light signaling components beyond the photoreceptors. The proposed Ph.D. project, therefore, addresses the functions of light signaling components in the moss Physcomitrella patens using genetic and molecular-biochemical approaches.
Functional comparison of trichome and root hair development in Arabis alpina and Arabidopsis thaliana
Trichome and root hair density are important for the adaptation of plants to environmental conditions. As in Arabidopsis thaliana both traits are regulated by and large the same regulatory network it is expected that its evolution faces some constraints. The goal of this project is to study the evolution of this gene regulatory network by comparing trichome and root hair patterning between A. thaliana and A. alpina at the functional and molecular level.
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).