Applications are now open for 11 PhD projects in the framework iof the iGRAD-Plant program – 

a PhD program for early career scientits with a bachelors degree 

Application Deadline: extended to May 22 2022

Shortlisted candidates will be invited to a selection workshop at HHU Düsseldorf in early July.

Starting date of the qualification year: Fall 2022

Application Requirements:

• Excellent Bachelor’s degree or equivalent in biology, biochemistry, genetics, microbiology computer sciences, quantitative biology or a related field.
• Please note: students holding a master’s degree are not eligible to apply for this program.
• Students who are now just starting a 2-year master’s study program (< 3 months into the program) are eligible to apply.
• Applicants who are not native speakers should demonstrate adequate competence of the English language by acceptable results of an internationally recognized test (e.g. TOEFL, IELTS).

Qualification Program

The iGRAD-Plant Program offers a comprehensive, interdisciplinary PhD training program in the fields of molecular plant sciences, plant genetics, synthetic biology, quantitative biology and computer sciences comprising a 1-year qualification period followed by a 3-year doctoral research period, with total funding up to four years. Obtaining a M.Sc. between both phases is possible. Successful applicants will be enrolled at HHU Düsseldorf and will benefit from a structured supportive program with shared supervision and training in a wide range of transferable and scientific skills.

Funding

The program provides every student with a tax-free fellowship of €861 per month during the qualification year. After the qualification year and the admission to PhD studies at HHU students are funded with a position (50-65% EG 13 TV-L pay scale) for 3 years.

All iGRAD-Plant fellows have to enroll as doctoral researcher at Heinrich Heine University. The social contribution fee is approx. €315 per semester (summer term 2022). The social fee includes free public transportation in the area of North-Rhine Westphalia.

Support 

Extensive administrative support (visa, housing, health insurance, enrollment) for international students via the Welcome Center of the HHU Junior and International Researcher Center.

Projects Available:

Project ID: 01

Iron regulation modules in the context of Fe resource allocation, seed sink strength and evolution in Arabidopsis thaliana

Supervising PI(s): Petra Bauer

Iron (Fe) is an essential metal for numerous electron transfer reactions in plants and thereby affects drastically photosynthetic activities, carbon sinks, plant growth and yield. Fe plays a vital role in oxygen transport in humans and is critical for quality nutrition. In angiosperms, Fe is mobilized and taken up by the root, subsequently allocated to different plant parts and cellular compartments and delivered to sinks like seeds and grains. This process is controlled by an Fe-regulated transcription factor (TF) cascade. Fe-regulated TFs target different clusters of co-expressed genes, that encode regulatory proteins of the cascade itself as well as metal homeostasis components, acting locally and long-distance in metal uptake from the soil and internal Fe resource allocation. Here, we will study mechanistic details how Fe resource allocation is triggered by the Fe regulation cascade and sink strength and the evolution of the Fe regulation modules in seed plants. Techniques of genetics, molecular biology, plant physiology, synthetic biology and computational analysis will be applied.

Project ID: 02

Computational analysis of resource allocation in photosynthesis under nutrient limitation

Supervising PI(s): Oliver Ebenhöh

Plants use photosynthesis to convert solar into chemical energy, which is then used to reduce and fix atmospheric carbon dioxide. Thus, the photosynthetic apparatus is absolutely essential for survival. On the other hand, constructing and maintaining the photosynthetic apparatus is also costly. The key enzyme RuBisCO alone makes up between 5 and 40% of total protein in plants, and thus represents a major nitrogen sink. Some proteins in the elctron transport chain have a rapid turnover time and thus maintenance requires considerable energy and mineral resources. Depending on the availability of mineral nutrients (in particular N, P, S, Fe, Mn), the resources to build and maintain the photosynthetic apparatus may be difficult to obtain.

In this project, we will employ mathematical models of photosynthesis and carbon fixation, previously developed in our group, to quantify costs associated with building and maintaining the components of the photosynthetic electron transport chain and the Calvin-Benson Cycle enzymes in dependence on nutrient availability. We will use the theoretical model to calculate optimal resource distributions to maximise photosynthetic efficiency and carbon fixation rate depending on the associated costs. Finally, we will combine these results to predict optimal compositions of the photosynthetic machinery in dependence on combinations of nutrient limitations. These results will support designing experiments to validate the model predictions and to test the hypothesis that resource allocation under nutrient limitation is optimal.

Project ID: 03

Resource allocation during biotic stress: Nutrition of fungal pathogens in plants

Supervising PI(s): Michael Feldbrügge, Vera Göhre, Florian Altegoer

Plants tightly control nutrient uptake and allocation for optimal growth, but infection with pathogens disturbs this fine-tuned balance. Therefore, an overarching goal is to unravel the molecular interaction of pathogens with the plant vasculature, i. e. the highways of water (xylem) and nutrient transport (phloem). In this project, we investigate economically important and genetically tractable smut fungi to understand how they use receptors and transporters to modify host nutrient allocation at the cellular level and the phloem for their own benefit. A starting point are membrane-bound virulence factors, which are essential for virulence of U. maydis. Combining genetics, infection assays and biochemistry with state-of-the art biosensors will show how metabolic re-routing is achieved with the help of fungal membrane factors.

Comparison to bacterial pathogens growing in the xylem studied in the group of W. Frommer on the one hand and iron acquisition studied by the group of P. Bauer will provide an overall picture of resource allocation plant-microbe interactions. Quantitative physiological data of nutrient fluxes will be integrated into metabolic models in collaboration with the other groups of the graduate school.

References:

Frantzeskakis, L.; Courville, K.J.; Pluecker, L.; Kellner, R.; Kruse, J.; Brachmann, A.; Feldbrügge, M.; Göhre, V. The plant-dependent life cycle of Thecaphora thlaspeos: a smut fungus adapted to Brassicaceae. Molecular Plant-Microbe Interactions 2017, 10.1094/mpmi-08-16-0164-r, doi:10.1094/mpmi-08-16-0164-r.

Courville, K.J.; Frantzeskakis, L.; Gul, S.; Haeger, N.; Kellner, R.; Heßler, N.; Day, B.; Usadel, B.; Gupta, Y.K.; van Esse, H.P., et al. Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors. New Phytol 2019, 0, doi:10.1111/nph.15692.

Wahl, R.; Wippel, K.; Goos, S.; Kämper, J.; Sauer, N. A novel high-affinity sucrose transporter is required for virulence of the plant pathogen Ustilago maydis. PLoS Biol 2010, 8, e1000303, doi:10.1371/journal.pbio.1000303.

Doehlemann, G.; Reissmann, S.; Assmann, D.; Fleckenstein, M.; Kahmann, R. Two linked genes encoding a secreted effector and a membrane protein are essential for Ustilago maydis-induced tumour formation. Molecular Microbiology 2011, 81, 751-766, doi:10.1111/j.1365-2958.2011.07728.x.

Project ID 04

Sugar fluxes in rice leaves infected by the bacterial blight bacterium Xanthomonas oryzae

Supervising PI(s): Wolf Frommer

Plants need to balance growth and pathogen defense. Pathogens infect plants primarily in order to gain access to the host as a source of nutrients required for reproduction. In the case of bacterial blight, the xylem pathogen Xanthomonas oryzae pv. oryzae  injects TAL (transcription activator-like) effectors (Tale) into the host, thereby triggering ectopic induction of host SWEET sucrose transporter genes in the xylem parenchyma¹. The virulence of Xoo depends on access to the sucrose that is released through this mechanism from the xylem parenchyma (XP)^2–4. Since the xylem does not produce sucrose and is not involved in sucrose translocation, a key question is where exactly the sucrose that is secreted during infection is coming from. Is the induction of SWEETs restricted to the xylem parenchyma, or can the TALe move through plasmodesmata (PD) to adjacent cells in the phloem. Alternatively, is sucrose transported via plasmodesmata or specific SWEETs  to the XP. To address these questions the following approaches are planned:

Aim 1: Single cell sequencing of rice leaves from uninfected and infected plants to identify XP-related processes and effects of the bacteria on adjacent cells. Analyze the effects on PD gene candidates and sugar transporter genes.

Aim 2: Test whether bacterial effectors injected into the XP stay cell-autonomous or move through PD to adjacent cells using GFP fusions and confocal microscopy. Block PD functions in rice leaves in XP (Casl3S in XP, BS, mesophyll)⁵. Use the OspoxA promoter to drive XP expression⁶.

Aim 3: Where does the sucrose come from? Deploy genetically encoded sugar sensors^7,8 driven form the XP promoter poxA in rice leaves. Characterize the effect of alterations to the phloem supply (local aluminum foil during infection, watch infection using SWEET reporter lines).

Comparison to fungal pathogens in maize studied in the group of M. Feldbrügge on the one hand and iron acquisition studied by the group of P. Bauer will provide an overall picture of resource allocation plant-microbe interactions. Quantitative physiological data of nutrient fluxes will be integrated into metabolic models in collaboration with the other groups of the graduate school.

Project ID 05

Mechanistic modeling of plant performance and evolution

Supervising PI(s): Martin Lercher

Plant performance is strongly influenced by interactions with abiotic factors, including climate, microclimate, and soil properties. Our group develops multi-scale computational models that estimate plant fitness from a mechanistic analysis of these connections, fully based on physical and chemical principles. They describe the interactions of water transport with detailed, molecular representations of photosynthesis and metabolism in a coarse-grained description of plant anatomy. This PhD project will extend the mechanistic models and apply them to model plant resource allocation, performance, and evolution in specific environments.

Project ID: 06

Turnover and cost-benefit analysis of photosynthesis

Supervising PI(s): Shizue Matsubara, Oliver Ebenhöh

Maintaining photosynthesis under adverse environments is a key factor for plant resilience and stability of crop production. While we have been witnessing remarkable expansion of knowledge and mechanistic understanding of stress response in photosynthesis, only a few attempts have been made to assess the costs and benefits of keeping photosynthesis up and running. Given the wealth of plant biodiversity adapted to a wide range of growth conditions, some plants may have evolved unique strategies to balance the trade-offs between maximization of resource acquisition and stress tolerance, which could be tapped into as genetic resources for plant breeding.

A critical knowledge gap in estimating the maintenance costs of photosynthesis is turnover of the components of photosynthetic machinery. Hence, this PhD project is aimed at gaining quantitative information on, and insights into, turnover of photosynthetic machinery to enable improved cost-benefit analysis of photosynthesis. To unravel genetic and environmental influence, experiments will be conducted using different genotypes and environmental conditions. The work will offer exciting opportunities to learn isotopic labeling technique in combination with mass spectrometry analysis. The results will be analyzed in close collaboration with metabolomics and proteomics laboratories as well as computational scientists doing photosynthesis modeling.

Project ID: 07

The evolution of resource allocation to plant cell wall polysaccharides

Supervising PI(s): Markus Pauly, MSU: Federica Brandizzi

Regulation of carbon allocation to polymers in the plant cell wall (Pauly lab, HHU; Brandizzi Lab, MSU). The regulation of depositing carbon into polysaccharides will be investigated using a synthetic biology approach. Known biosynthetic genes from various plant species will be expressed in yeast and the production of the polymers monitored. Enhancement of carbon wall deposition through mutagenesis of those genes as well as protein-protein interactions to establish metabolic channels will be assessed.

References:

Kim SJ, Chandrasekar B, Rea A, Danhof L, Zemelis-Durfee S, Thrower N, Shepard Z, Pauly M, Brandizzi F, Keegstra K, 2020, The synthesis of xyloglucan, an abundant plant cell wall polysaccharide, requires CSLC function, PNAS, 117 (33), 20316-20324, doi:10.1073/pnas.2007245117

Project ID 08

Role of reproductive sink size as a driver for resource allocation in barley and Arabidopsis

Supervising PI(s): Rüdiger Simon

The initiation and development of seeds requires extensive resource allocation over prolonged time periods. However, the role of reproductive sink size (RSS) as a driver for resource allocation and photosynthetic activity remains underinvestigated. In the first funding period, we have used prior knowledge on meristem regulation from Arabidopsis to identify key regulatory signalling networks in barley that control meristem activities and, ultimately, the production of floral meristems and seeds. We generated a range of mutants that exhibit, compared to wildtype, altered floral meristem numbers, inflorescence meristem sizes and differ in seed number per inflorescences. The mutated gene functions will be analysed in detail to understand how meristem activities are controlled and coordinated along the inflorescence axis. Reporter lines for hormone signalling pathways and for sugar metabolites will be established in barley to identify bottlenecks for meristem number and productivity, and to infer changes in RSS feedback upon photosynthetic activity in leaves.

References:

Kirschner, G.K., Stahl, Y., Imani, J., von Korff Schmising, M. and Simon, R. (2018) Fluorescent reporter lines for auxin and cytokinin signalling in barley (Hordeum vulgare). Plos ONE doi.org/10.1371/journal.pone.0196086

Project ID: 09

Isolation of alleles influencing resource allocation in barley

Supervising PI(s): Benjamin Stich

Barley is characterized by high levels of intra-specific diversity and adaptation to environments both stress-prone and resource-rich, and to environments characterized by all levels of competition. These features, together with the available genomic resources, make it an attractive model for understanding resource allocation. We have developed the barley double round robin population (Casale et al. 2021). The parents of this population which comprise landraces but also registered varieties differ considerably with respect to many characters involved in resource allocation such as flowering time but also sink capacity. This as a good starting point to isolate the underlying allelic variants. In addition, the pleiotropic effect of the variants on other agronomic characters as well as their expression and adaptive potential under various environmental conditions will be studied in field but also plant growth chamber experiments.

Project ID 10

Inducible CAM in T. triangulare – adaptation of resource allocation to altered environments and its genetic basis

Supervising PI(s): Andreas Weber

Crassulacean Acid Metabolism (CAM) represents the most water use efficient mode of photosynthesis in land plants. T. triangulare can outlast episodes of drought by ABA-mediated  induction of CAM and return to C₃ upon rewatering (Brilhaus et al., 2016; Maleckova et al., 2019). Our project aims at (i) quantifying the re-allocation of resources from C₃ to CAM photosynthesis under drought and (ii) to unravel the molecular mechanisms and regulatory networks underpinning reversible CAM induction during drought. We will collaborate with the Zurbriggen lab on synthetic reconstruction of regulatory networks in orthogonal systems, with the Matsubara lab on tracing the turnover of resources by isotope labeling, and with the Lercher and Ebenhöh groups on computational analysis of resource allocation between different modes of photosynthesis.

References:

Maleckova E, Brilhaus D, Wrobel TJ, Weber APM (2019) Transcript and Metabolite Changes during the Early Phase of ABA-mediated Induction of CAM in Talinum triangulare. J Exp Bot 70 (22), 6581-6596

Brilhaus D, Bräutigam A, Mettler-Altmann T, Winter K, Weber APM (2016) Reversible Burst of Transcriptional Changes During Induction of Crassulacean Acid Metabolism (CAM) in Talinum triangulare. Plant Physiol 170(1): 102-122.

Project ID: 11

Synthetic reconstruction approach in animal cells for the study of growth and development signalling networks

Supervising PI(s): Matias Zurbriggen, Oliver Ebenhöh, Andreas Weber, MSU: Erich Grotewold, Susanne Hoffmann-Benning

Plant signaling networks regulating growth and development integrate a complex mesh of exogenous (environmental) and endogenous (genetic, metabolic, developmental) input signals, and information processing functions with extensive crosstalk. Current genetic and biochemical approaches provide a complete description of the signaling cascades in terms of components, connectivity, and function. However, a thorough quantitative understanding is precluded by the combinatorial genetic complexity and multifactorial dynamic interactions posing experimental constraints.

In this project, we will overcome current experimental limitations by implementing a synthetic biology approach, comprising mammalian and plant cells, optogenetics, CRISPR/Cas-based technologies, and 3D-Bioprinting which jointly provide alternative theoretical-experimental resources. This strategy will yield a quantitative understanding of mechanistic and regulatory principles involved in light and hormone signaling networks leading to decisions on growth and development.

We will here perform a partial reconstruction of the signalling networks in a heterologous/orthogonal mammalian cell system, thereby simplifying the protein environment, limiting redundancy, and avoiding interactions/crosstalk with endogenous components that affect the analysis in planta. The implementation of numerous synthetic biology tools, reporters and readout system, and advanced microscopy techniques (FRET-FLIM, fluorescence anisotropy, high-content multi-well confocal fluo microscopy) available in mammalian cells will yield experimental quantitative data on protein-protein interactions and signaling hub regulatory mechanisms. These data will be mathematically modelled to obtain a structural and functional description of the networks. The models will aid the design of targeted biochemical and physiological experiments in plant cells and in planta to determine and validate the mechanistic insights obtained.

The work in plants include the use of optogenetic approaches and CRISPR-Cas-based technologies for the targeted and precise spatio-temporal control over gene expression and editing of the genes of interest involved in the regulation. 3D-Bioprinting in defined spatial arrangements of mammalian and plant cells equipped with synthetic signalling networks and the above-mentioned molecular tools will allow the study of the cell-cell communication processes involved and the effect of the cellular environment in the spatio-temporal context-mediated regulatory networks.

The unique combination of the studies in the heterologous platform and in planta, and the use of advanced molecular and cellular technologies will provide a quantitative understanding of the phenotypic effects and instruct the targeted regulation of the signaling networks towards an optimized performance, i.e. resource allocation and use, during growth in a varying environment.

References:

Andres J, Saadat N, Samodelov SL, Al-Babili S, Ebenhöh O/Zurbriggen MD Combining quantitative theoretical-experimental approaches towards understanding strigolactone signalling dynamics (2022) Submitted

Beyer HM, Juillot S, Herbst K, Samodelov SL, Müller K, Schamel WW, Römer W, Schäfer E, Nagy F, Strähle U, Weber W and Zurbriggen MD (2015) Red light-regulated reversible nuclear localization of proteins in mammalian cells and zebra fish. ACS Synthetic Biology 4(7) DOI: 10.1021/acssynbio.5b00004 Cover Article Issue July 2015

Blanco-Touriñan N, Legris M, Minguet EG, Costigliolo-Rojas C, Nohales MA, Iniesto E, Garcia-Leon M, Pacin M, Heucken N, Blomeier T, Locascio A, Cerny M, Esteve-Bruna D, Diez-Diaz M, Brzobohaty B, Frerigmann H, Zurbriggen MD, Kay SA, Rubio V, Blazquez MA, Casal JJ and Alabadi D (2020) COP1 destabilizes DELLA proteins in Arabidopsis. Proceedings of the National Academy of Sciences (PNAS) USA 117(24):13792-13799 DOI: 10.1073/pnas.1907969117

Graz R, Brumbarova T, Ivanov R, Trofimov K, Tünnermann L, Ochoa-Fernandez R, Blomeier T, Meiser J, Weidtkamp-Peters S, Zurbriggen MD and Bauer P (2019) Phospho-mutant activity assays provide evidence for alternative phospho-regulation pathways of the transcription factor FIT. New Phytologist 225(1):350-267 DOI: 10.1111/nph.16168

Ochoa-Fernandez R, Abel NB, Wieland F-G, Schlegel J, Koch L-A, Miller JB, Engesser R, Giuriani G, Brandl SM, Timmer J, Weber W, Ott T, Simon R and Zurbriggen MD (2020) Optogenetic control of gene expression in plants in the presence of ambient white light. Nature Methods 17:717-725 DOI: 10.1038/s41592-020-0868-y

Samodelov SL, Beyer HM, Guo X, Augustin M, Jia K-P, Beyer P, Weber W, Ebenhöh O, Al-Babili S and Zurbriggen MD (2016) StrigoQuant: a genetically encoded biosensor for quantifying strigolactone activity and specificity. Science Advances 2:e1601266 DOI: 10.1126/sciadv.1601266

Samodelov SL and Zurbriggen MD (2017) Quantitatively understanding plant signalling: novel theoretical-experimental approaches. Trends in Plant Science  22(8) DOI: 10.1016/j.tplants.2017.06.006

How To Apply:

• Application form completely filled-in. Please read the guide „how to fill the application form“ before doing so
• A Curriculum Vitae detailing education, training, and previous research experience
• Transcripts of previous study, including credit hours, marks obtained and copies of relevant diplomas and degrees in English or German
• Documentation of proficiency in the English language, such as TOEFL, IELTS, Duolingo (can be waived for native speakers or if the university education was conducted in English)
• Two letters of reference from previous supervisors, send directly by the referee to: igrad-plant@hhu.de. 

Please send a complete electronic copy of your application as a single PDF (file size not exceeding 5 MB!) by email to igrad-plant(at)hhu.de. 

Do not send originals, documents will not be returned. We will request certified copies of documents once a selection of successful candidates has been made.

Contact

iGRAD-Plant Coordinator

Dr. Petra Fackendahl

Institute of Plant Biochemistry
Universitätsstr. 1
40225 Düsseldorf Gebäude: 26.24
Etage/Raum: U1.066
40225 Düsseldorf

+49 211 81-10588 E-Mail senden