Please note that only complete applications are accepted! Qualified candidates should send their complete application including
citing reference number 129.22-3.1 no later than June 06, 2022 by e-mail (one single pdf-file) to application[at]ceplas.de.
Please click on the "more" button to get more information about the projects and the qualifications needed.
1. Mechanisms and conservation of roles of trehalose 6-phosphate in plant developmental progression
Developmental decision making in plants is closely integrated with primary metabolism. In Arabidopsis thaliana, the metabolite trehalose 6-phosphate plays a signaling role in mediating between sucrose metabolism and developmental progression of meristems. However, the biochemical mechanisms by which it functions and the extent to which its roles are conserved in plants showing different patterns of growth and development are unknown. Here, we propose to use cutting-edge phosphoproteomics approaches to explore the mechanism of action of trehalose 6-phosphate in meristems during floral transition and comparative genetics to determine whether its functions are conserved in perennial species closely related to A. thaliana.
Qualifications needed: PhD in plant molecular biology, plant physiology, plant development or similar discipline. Knowledge on flowering and branching regulation in Arabidopsis or expertise on proteomics and Arabidopsis growth and handling advantageous.
Contact person: Franziska Fichtner / George Coupland
2. Just coincidence? How similar signals convey different information during systemic light signaling
Plants are constantly subjected to external stimuli, i.e., due to variable water availability, herbivore attack or different light regimes. Selective sensing of and appropriate response to a given stimulus is therefore pivotal for the plant to ensure survival and reproduction in changing environmental conditions. To this end, plants developed a complex perception and transmission system, allowing them to systemically communicate a local stimulus to distal, unaffected parts of the plant in order to acclimate or prime the distal tissue to the stimulus. Intriguingly, systemic responses seem to rely on the same type of propagating signals, which can be broadly categorized as electric, chemical (i.e., calcium) or hydraulic. Focusing on systemic light signaling, we want to analyze, how plants can distinguish different external stimuli and generate specific responses to them, albeit relying on similar signals for systemic transmission.
Qualifications needed: PhD degree in biology or related life sciences
Contact person: Michael Wudick
3. Identification and 3D modeling of gene regulatory networks that determine leaf anatomy and physiology in C3-C4 intermediate Brassicaceae.
C3-C4 intermediate (also called C2) photosynthesis, an evolutionary precursor to C4 photosynthesis, independently and convergently evolved 5-times in the Brassiceae. C3-C4 intermediates display a low CO2 compensation point and C4-like leaf anatomical features, such as an enlarged bundle-sheath cross-sectional area and the accumulation of large numbers of centripetally arranged chloroplasts and mitochondria in bundle sheath cells. Along with altered photosynthetic physiology and leaf anatomy, gene expression patterns are modified, such as bundle-sheath-specific expression of genes encoding enzymes of photorespiration. To date, it is unknown how the characteristic leaf anatomy of C3-C4 intermediates is established and which gene-regulatory circuits govern this process. The five independent evolutionary origins of the stereotypic C3-C4 leaf anatomy, biochemistry, and physiology in the Brassicaceae provides a unique opportunity to unravel these networks. In this project, we will combine microscopy, cell biology, and single-cell approaches in combination with computational biology to identify key regulators that determine C3-C4 anatomy.
Qualifications needed: Plant cell biology, molecular biology, computational biology
Contact person: Andreas Weber
4. Genetic and physiological characterization of a novel leaflet number QTL in C. hirsuta
Seed plant leaves show considerable variation in their shapes. However, the mechanistic underpinnings of this variation have only just begun to be understood and its physiological significance also remains enigmatic. Using comparisons between the simple leaf model plant Arabidopsis thaliana and its relative Cardamine hirsuta, that bears complex leaves subdivided to leaflets, we have begun to unravel the genetic basis for variation in leaf shape both within and between species. Our findings also allow an understanding of the physiological significance for this variation. Using QTL analysis, we found that age-dependent leaf development pathways underlie a major component of natural variation for leaf complexity in C. hirsuta. These observations suggest that studying complex leaves has significant potential for understanding and manipulating leaf developmental inputs in to photosynthesis and plant performance. Such work will be the focus of this proposal. See Cartolano et al, PNAS 2015, Kierzkowski et al, Cell 2019.
Qualifications needed: Plant molecular biology, plant physiology/photosynthesis, QTL analysis
Contact persons: Miltos Tsiantis
5. Photosynthesis phenomics
Photosynthesis is considered an important plant trait that is quantitative and dynamic at the same time. Phenotyping platforms have been designed and built worldwide for characterization of photosynthesis in controlled conditions to understand the relationship between genotype, phenotype and environment. In the face of urgent challenges posed by climate change, there is a growing emphasis on "environment" in this relationship. To further our understanding of photosynthesis in relevant field conditions, and to select genetic variants with improved photosynthetic efficiency under those conditions, we will establish phenotyping platforms that allow in situ capturing of photosynthesis traits under simulated field-like conditions and climate scenarios. Phenotypic data thus obtained will be complemented by analyses of metabolome, transcriptome and proteome to enhance our mechanistic understanding and realize genome-to-phenome mapping. Experiments will be designed and analyzed together with computational modeling group towards simulating G x E interactions in model plants and crop species.
Qualifications needed: Experience in photosynthesis measurements, plant physiology, plant phenotyping, team work, mobility
Contact persons: Shizue Matsubara
6. Computational modeling of Fe-regulatory networks
Cellular signaling can be amplified in positive feed-forward loops or become inhibited under a negative feed-back. Nutritional cues often elicit complex configurations of coherent and incoherent regulation. The micronutrient iron (Fe) is required for many redox and electron transfer reactions. Fe affects photosynthesis and nutrient assimilation and determines plant nutritional values. During their growth, plants are challenged to take up Fe from the soil, store it, transport and allocate it to sink organs, in accordance with growth dynamics and environmental stress as experienced under climate change. An intricate gene regulatory network controls Fe homeostasis. The aim of this project is to combine large-scale data to reconstruct mechanistic models and simulate the Fe-regulatory response networks. Regulatory circuits are experimentally validated in targeted assays.
Qualifications needed: Modeling, quantitative biology, mathematics, transcription factor, gene expression networks, gene expression
Contact persons: Petra Bauer, Nadine Töpfer, Jedrzej Jakub Szymanski (IPK)
7. Antimicrobial effectors secreted by plant-colonizing fungi and their impact on microbial communities in natural soils
Plant tissues are colonized by a wealth of micro-organisms, including bacteria and fungi. To colonize plant hosts, fungi employ various mechanisms, including the secretion of functionally diverse effectors. Verticillium dahliae was recently shown to secrete effectors with antimicrobial activities, in order to modulate plant microbiota. By inhibiting the growth of microbial competitors, these effectors facilitate fungal colonization of plant roots. Here, we aim to identify antimicrobial effectors secreted by a ubiquitous family of soil-borne fungi, and functionally characterize those with strong influence on microbial communities in soil, eventually impacting plant performance. We will therefore (1) develop an algorithm predicting antimicrobial activity of fungal effectors; (2) assess how fungi secreting different sets of antimicrobial effectors impact microbial communities in different natural soils. The expected outcome of this project is the discovery and validation of effectors shaping microbial communities in soil, thus playing key roles in fungal fitness and edaphic adaptation.
Qualifications needed: microbiology, soil communities, genomics, machine learning, gnotobiotic experiments, ecology
Contact person: Bart Thomma
8. Host-specific regulation of effector gene expression in mutualistic root endophytic fungi
Effector proteins are used by plant-associated fungi to facilitate colonization via effector-triggered susceptibility and manipulation of host defense and metabolism. Past research has been focused on the identification and elucidation of the function of effectors from pathogenic fungi during colonization of one plant host species. By comparison, knowledge of how beneficial fungi regulate the expression of effector genes and their function in different plant hosts and in response to other microbes has been lagging. Recent studies have illustrated the role of various transcription factors, chromatin-based control and effector epistasis in regulating effector expression in the host plant. Here we propose to use DAP-seq and RNA-seq to generate cistrome maps for Serendipita indica and S. vermifera, two closely related beneficial fungal symbionts from the order Sebacinales that inhabit the roots of phylogenetically diverse plant species. Machine learning approach and reverse genetics will be additionally used to produce complementary and comprehensive data that will help dissect fungal effector regulation in planta and during microbial competition. Improved knowledge of effector regulation during confrontation with other microbes and in different plant hosts and edaphic conditions is likely to assist in providing novel plant protection strategies and in the generation of more resilient fungal strains with enhanced root colonization and growth promotion abilities.
Qualifications needed: bioinformatics; trancriptomics; machine learning; amplicon sequencing
Contact person: Alga Zuccaro
9. Non-invasive genetic mapping of nutrient-related root responses with single-cell resolution
Plant roots sense their (a)biotic environments and integrate this into their architecture. While we have some understanding of the effects that determine this, we lack a spatiotemporal framework for how root-environment interactions determine form and function at the single-cell level. This is essential to optimize nutrient uptake mechanisms. We have created a physiological imaging platform which allow us to study this in detail. Our setup is based on a vertical confocal microscope and fluidics-chambers, which allow us to study root growth under a variety of conditions continously over time spans of upto two weeks . The main aim of this project is to map how roots coordinate growth with nutrient transporter expression at a single-cell level under abiotic stress conditions in presence or absense of microbes. This will likely lead to novel agriculturally applicable insights into how root cells communicate and integrate signals into a holistic whole root-level response.
Qualifications needed: quantitative imaging, Nutrient physiology, Root development, Statistics, Plant-microbe interactions
Contact person: Tonni Grube Andersen
10. Metabolic interactions of plants and root-associated microbes via the pipecolate pathway
The pipecolate metabolic pathway plays a crucial role in the activation of systemic acquired resistance in the plant shoot, but its function in roots is unknown. This project will investigate the interplay between root-associated microorganisms and plants on the basis of complementary, pipecolate pathway-related metabolic activities of these interaction partners. Specifically, it will examine whether 4-hydroxylation of plant-derived pipecolates by fungal oxygenases is a precondition for the accommodation of soil-born fungi in plant tissue. It will also identify and biochemically characterize novel pipecolate-metabolizing activities of rhizosphere-associated and root endophytic bacteria and examine whether pipecolate synthesis mediated by a particular microbial soil composition can enhance pathogen resistance in the shoot. Conversely, it will specify edaphic environments that activate plant pipecolate metabolism in roots, investigate its biological function under these conditions and examine whether pipecolate pathway products contribute to shaping the composition of the root microbiome.
Qualifications needed: PhD in biology, biochemistry or a related life science. Experiences in plant molecular biology, biochemistry, small metabolite analysis, plant-microbe interactions and/or microbiology are advantageous
Contact person: Jürgen Zeier
11. DryCell - uncovering the cell biology of desiccation and rehydration in plant roots
In this project, we aim to elucidate the subcellular processes occurring in plant roots exposed to extreme water stress conditions and how roots of resurrection plants are able to survive complete desiccation and rapid rehydration. We will develop a microchamber-based setup that addresses the optical challenges of dry cell imaging and a genetically encoded biosensor that reports changes in intracellular osmolarity. Using these techniques, we will study the mechanisms underlying the cell-protective functions of proteins linked to desiccation resistance and explore their potential to improve drought tolerance in model and crop plants.
Qualifications needed: We are looking for a plant cell biologist with proficiency in live-cell, fluorescence and confocal imaging techniques; profound knowledge in optics; demonstrated tool development skills. A strong background in molecular biology is required. Previous experience in plant drought stress or with resurrection plants would be a plus.
Contact person: Guido Grossmann
12. Reconstruction of carbon allocation towards multiple plant cell wall sinks in yeast and cyanobacteria
Photosynthetically assimilated carbon is deposited into sinks of which the plant cell wall is the largest naturally occurring one, not only at the cellular level but also considering the earth's biosphere. The proposed project aims at identifying factors that play a role in regulating carbon allocation from the central carbon pool towards plant cell wall sinks by utilizing forward genetics in plant-polymer producing yeast strains (Pichia pastoris). Another aim is the reconstruction of wall C-sinks in a photosynthetic unicellular organism - cyanobacteria. These approaches will provide us with mechanistic and quantitative data on cell wall production and C-allocations and will help to identify plant factors involved in the regulation of C-allocation towards this dominant sink.
Qualifications needed: Molecular biology, sterile work with organisms, biochemistry, carbohydrate analytics
Contact person: Markus Pauly
13. Synthetic leaf-like structures to study differentiation and developmental trajectories/programs
We will develop and implement synthetic approaches to reconstruct and engineer synthetic tissues with a custom-designed architecture, vasculature, anatomy and biochemical and physiological functionality. Our approach will facilitate the study of cell trajectories for anatomy, vasculature and photosynthetic patterning, function and development during leaf (and root) growth. For this we will integrate novel technologies including 3D Bioprinting, microfluidics, optogenetic control of cell fate and tissue culture, single-cell RNASeq and advanced microscopy. The in vitro synthetic cell-environment model system for the 4D targeted differentiation of plant cells in the absence of a tissue context will be first applied to the study of fundamental questions regarding the inner workings of differentiation-anatomy-function relationship/interactions in the development of photosynthetic tissues and root architecture. The engineering of synthetic leaf-like structures and other tissues will enable not only to test mechanistic hypotheses but also the design of new traits towards achieving smart plants.
Qualifications needed: Plant cell culture, synthetic biology, biochemistry
Contact person: Andreas Weber / Matias Zurbriggen
14. Synthetic biology reconstruction and optogenetics approach towards a quantitative analysis of plant signalling networks
We will design, engineer and implement an experimental-theoretical synthetic biology framework for the quantitative understanding, control and engineering of complex plant molecular signaling networks regulating cellular and leaf and root tissue differentiation, development and function. The project comprises two approaches: i) reconstruction of plant signaling pathways in orthogonal, mammalian systems to carry out quantitative studies on pathway architectures, which are otherwise technically challenging to perform on a cellular level in planta due to the molecular complexity of signaling networks. It enables rapid testing of genetic diversity of cellular components and their directed evolution on a scale/throughput rate that is not possible in planta. It also yields high-throughput quantitative data that will be used to generate dynamic mathematical models, which will inform how the effects of genetic variation at the level of gene regulatory networks translate into differential pathway function and hence phenotype, and be used to instruct experimental in planta studies; ii) Optogenetics in combination with CRISPR-Cas-based techs in multiplexing set ups will provide maximized control and specificity of activity of target regulators in planta, in terms of spatial resolution, temporal control, quantitative levels, and reversibility. Overall, this approach will enable the targeted investigation of networks, functional studies, and ultimately to obtain novel traits for crop improvement.
Qualifications needed: Plant and mammalian cell culture, synthetic biology, optogenetics
Contact person: Matias Zurbriggen
15. Towards a synthetic leaf - vasculature pattern
The vasculature/grid architecture in leaves is investigated. A modelling and synthetic biology approach is used to create synthetic leaves with spatially defined vasculature architectures. After assessing the physiology of such a synthetic leaf, the vasculature grid algorithm will be modified and a more optimal vasculature grid retested.
Qualifications needed: Molecular biology, sterile working with cell cultures, programming, modelling
Contact person: Markus Pauly / Oliver Ebenhöh
16. Haplotype diversity of cultivated potato
Potato is among the three most important food crops worldwide. But despite its importance, our knowledge of the genomic makeup of modern potato cultivars is negligibly small as the highly divergent, autotetraploid and partially inbred genomes challenge conventional strategies for genome analyses. We recently developed a new method to assemble all four haplotypes of autotetraploid genomes using single-cell-based genotyping of individual pollen grains. We used this method to generate the first fully phased, chromosome-level assembly of a tetraploid potato cultivar. In this project, the selected candidate will (i) contribute to the genome assembly of selected cultivars that were commonly used in the pedigrees of many modern cultivars, (ii) develop computational tools to analyze the diversity in modern cultivars based on the newly assembled haplotypes and (iii) validate this approach by analyzing recombinant pollen genomes.
Qualifications needed: Experiences in NGS analysis, bioinformatics, programming, HPC, Linux
Contact person: Korbinian Schneeberger
17. Modelling the crosstalk between phytohormone signalling and metabolism
Phytohormones trigger responses to environmental changes and stresses and initiate the transition between developmental stages. Phytohormones activate specific signalling cascades that then result in changed expression of key genes responsible to adapt the cellular behaviour according to the experienced stimulus. The various phytohormone signalling pathways cross-talk through a complex interconnected protein-protein interaction network.
So far, most experimental and theoretical investigations of phytohormone signalling focus on single environmental cues and isolated pathways. With our increasing understanding on the molecular mechanisms of the single hormone signalling pathways, we are now in a position to study phytohormone signalling as a systemic process and investigate its integration with metabolism and plant development.
In this project, we will develop integrated mathematical models, which provide a theoretical framework in which to interpret and understand experimental data, aiming at understanding how environmental and metabolic cues affect adaptive and developmental processes and vice versa.
Qualifications needed: Mathematical Modelling, Differential Equations, Metabolic Control Analysis, Calculus, Linear Algebra
Contact person: Oliver Ebenhöh
18. Impact of drought on the secondary cell wall of poplar xylem, a multi-disciplinary approach
Plants, ranging from agricultural and food crops to trees, are drastically impacted by climate change induced drought. Several factors of plant mortality due to drought have been identified. These include failure of the transpiration stream and hydraulics properties, and susceptibility to pests, both strongly relying on the properties of the secondary cell wall of xylem. In this project, we will develop a multi-scale modelling approach to understand how the microscopic biochemical and structural modifications of the secondary cell wall induced by drought impact the water transport in the xylem, and the recalcitrance to saccharification properties. We will first simulate the biosynthesis of the secondary cell wall using stochastic simulations before investigating the hydraulics of the system in the framework of mechanobiology, and performing plant cell wall degradation thanks to a previously developed model. Experimental data by collaborating partners will be systematically used to feed into the model and for comparison.
Qualifications needed: Computational Biophysics; Mechanobiology; Stochastic simulations; C++ programming; Excellent command of English
Contact person: Adélaïde Raguin
19. DeepCRE - deep learning applications for identification and functional annotation of cis-regulatory elements in crops
This project combines experimental expertise of the Hartwig (MPIPZ) and Schippers (IPK) labs with bioinformatics expertise of Usadel lab (FZJ/HHU), and machine learning methods of Szymański lab (IPK) for improvement of identification and annotation of plant cistrome. We will combine cutting edge genome-scale DNA binding assays with deep learning algorithms and a large public data resource to enable causal linking between gene regulatory sequences, binding of transcription factors and expression of downstream genes. A dedicated database and software packages will be generated.
Qualifications needed: Machine learning, artificial neural networks, DNA binding assays, RNA-seq analysis, gene regulatory networks
Contact person: Björn Usadel, Jedrzej Szymanski, Thomas Hartwig, Jozefus Schippers
20. The contribution of off-target transcription factor binding site on covariation between seed dormancy and flowering time
Genetic studies of complex traits in animals and plants have shown that trait variation is controlled by thousands of loci. The heritability of these traits appears to localize to non-coding regions, including transcription factor binding sites (TFBS). Are there genetic variants in non-coding loci throughout the genome that create novel TFBS, which do not control gene expression directly? If such sites exist, can they work as sink loci, sequestering transcription factors and decreasing the total amount available to regulate genes elsewhere in the genome? We propose to test this hypothesis by combining information on gene expression, ChIP-Seq and population variation in two complex plant traits, flowering time and dormancy, that are both partly regulated by the transcription factor FLC. The project will establish the contribution of a non-canonical molecular component to complex traits in higher organisms, breaking the dogma of a linear gene-transcript-phenotype relationship.
Qualifications needed: Plant Breeding, Statistical or quantitative genetics
Contact person: Juliette de Meaux
21. A multi-scale model to predict productivity improvements from modifications of plant anatomy, resource allocation, and protein activities
Varieties of a given crop species differ in details of anatomy and physiology, such as the abundances and activities of proteins in different cell types. A variety’s productivity will depend on environmental parameters such as temperature, rainfall, and soil type, such that different varieties are optimally productive in different environments. In this project, we aim to develop a computational framework that can quantify the interactions between plant anatomy and physiology and the growth environment. Our ultimate goal is a model that indicates genetic modifications that would optimize a given crop for an intended growth scenario.
Qualifications needed: PhD in Physics, engineering, or a related subject; experience in computational modeling and optimization
Contact person: Martin Lercher