The PhD Research Projects

PhD Research Project 1

Protein homeostasis during pollen development at higher temperatures

Project description

The regulation of protein and membrane homeostasis is interlinked to environmental conditions. For example, abundance and efficiency of transport complexes in the different endomembranes is dependent on environmental conditions and heat inducible HSPs are involved in recycling of preproteins under stress. In parallel, most transport systems have a multi-component architecture, and often more than one gene is found to encode for the individual components. The project aims to decipher the components involved in adaptation of protein distribution and homeostasis at high temperatures in pollen. This will include the analysis of the intracellular protein distribution system in pollen in general. Thereby, the objectives are:

1) Identification of translocon components involved in transport and translocation processes in pollen,
2) analyzing their response to environmental changes, and
3) description of their functional interplay with the regulatory network in pollen thermotolerance.

This work will include molecular, biochemical and cell biological methods.

Where

The group of Enrico Schleiff, Institute of Molecular Biosciences, Molecular Cell Biology of Plants, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Campus Riedberg, Germany, schleiff@bio.uni-frankfurt.de, +49 (0)69 79829287.

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PhD Research Project 2

The role of epigenetic modification in acclimation to heat stress in tomato

Project description

Induced tolerance to heat stress (HS) has been shown to be heritable within and over generations, suggesting the involvement of epigenetic control. Understanding epigenetic processes in pollen thermotolerant plants requires the description of the changes of stress-induced gene expression associated with alterations in DNA methylation and histone modifications; the acquirement of these changes during first stress experience; and the relation of the changes to later stress incidents. Thus, the project will focus on the question which epigenetic modifications lead to the acquisition of HS tolerance. The objectives are:

1) to determine the relation between HS regime and heritability of the induced tolerance,
2) to identify mitotically and meiotically stable HS-induced DNA methylation patterns, and
3) to correlate methylation patterns to the observed changes in gene expression and heat tolerance.

In this project high-throughput genomic techniques and other molecular biology tools will be applied.

Where

The group of Ivo Rieu, Radboud University of Nijmegen, Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands, i.rieu@science.ru.nl, phone: +31 (0)24 3652761.

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PhD Research Project 3

Hsf-Hsp interaction and function in tomato anthers and pollen

Project description

The interaction between the regulatory intracellular networks is a major element of stress responses leading to pollen thermotolerance (PTT), but the function of components involved is not well characterised. The project will focus on generation of GM plants with pollen-specific expression or knock-down of particular genes involved in PTT. The objectives are:

1) to prove the activity of suitable promoters in planta, with respect to cell/tissue specificity and HSR,
2) to analyze the influence of altered Hsf and Hsp expression on PTT specifically, and
3) to investigate the influence on plant growth, development and stress tolerance in general.

Analysis of phenotypical and physiological parameters requires the application of genetic, molecular biological and physiological approaches.

Where

The group of Celestina Mariani, Radboud University of Nijmegen, Department of Molecular Plant Physiology, Institute for Water and Wetland Research, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands, c.mariani@science.ru.nl, phone: +31 (0)24 3652773.

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PhD Research Project 4

The role of hormones and pollen-specific heat stress response genes in pollen thermotolerance

Project description

HSFs, chaperones and genes involved in hormone signaling and carbohydrate metabolism are involved in developing pollen HSR. Several of the identified pollen-expressed HSR genes are homologues of Arabidopsis genes that are expressed exclusively or mainly in pollen. These include a specific member of the Hsp90 chaperone family, genes that are involved in Ca2+-dependent signaling and vesicle trafficking, suggesting that maturing microspores may recruit available factors, including signaling network components used for maintaining pollen-specific functions. The project will target the activity of Hsfs during thermotolerance acquisition and their crosstalk with other, hormone based signaling pathways. The objective is to characterize the involvement of

1) Pollen-specific genes recruited for coping with heat stress.
2) Crosstalk between the HSF regulatory cascade and hormone (ethylene) signaling.

The project involves methods of molecular biology, plant physiology and microscopy.

Where

The group of Nurit Firon, The Agricultural Research Organisation of Israel - Volcani Centre, Department of Vegetable Research, Institute for Plant Sciences, 50250 Bet Dagan, Israel, Vcfiron@volcani.agri.gov.il, +97 239683735.

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PhD Research Project 5

Production and analysis of mutants in HSF and HSP genes

Project description

The over-expression of HSP genes in transgenic organisms was demonstrated to improve the tolerance to several abiotic stresses, but the effect of heat stress on pollen vitality produced by transgenic plants over-expressing HSP genes was poorly investigated so far. Thus, the project will aim at identification and analysis with respect to pollen thermotolerance of HSF and HSP mutants in tomato. The objectives are:

1) to verify that the genetic modifications will give beneficial effects on pollen under elevated heat stress and
2) to identify new allelic variants of HSFs or HSPs by the TILLING approach and to explore the influence of these mutants on PTT.

The project involves plant genetics, plant molecular biology and plant physiology, including high-throughput screening approaches.

Where

The group of Rina Iannacone, Metapontum Agrobios S.R.L., Strada Statale Ionica 106 KM. 448,2, Frazione di Metaponto SNC, 75010 Bernalda, Italy, Riannacone@agrobios.it, +39 0835740237.

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PhD Research Project 6

Metabolomics of thermotolerant tomato lines

Project description

Environmental stress leads to an altered or even disrupted metabolism in plants. Reprogramming of gene expression during heat acclimation leads to production of proteins and metabolites required to achieve a new state of homeostasis; and changes of three types of metabolites can be envisaged: i) signal transduction molecules, ii) compounds involved in acclimation; iii) products of disrupted pathways. Remarkably little is known of the metabolic changes associated with thermotolerance in crops or in developing anthers and pollen. A selection of tomato cultivars with contrasting pollen thermotolerance and specific mutants will be analysed for metabolic changes associated with heat acclimation to obtain insight in metabolic processes in developing tomato anthers and pollen. The objectives are

1) to elucidate the metabolic and genetic basis underlying pollen thermotolerance,
2) generation of Near Isogenic lines (NILs) by crossing with wild relatives of tomato and analyzing metabolomic profiles and pollen thermotolerance in populations derived from this.

The project involves plant genetics, molecular biology, plant physiology, and advanced metabolomic profiling approaches.

Where

The group of Arnaud Bovy, Wageningen Unversity, Department of Plant Sciences, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands, arnaud.bovy@wur.nl, +31 317480762.

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PhD Research Project 7

Proteomics of pollen thermotolerance - high throughput screening for protein markers and protein modifications

Project description

The identification of proteins as BIOMARKER is a major goal of molecular methods assisting plant breeding. The requirements for this strategy are a high sample throughput for the initial discovery and a subsequent high throughput analysis of the BIOMARKER in hundreds or thousands of plant lines. The PhD student will investigate proteomic differences in pollen of distinct tomato lines and establish methods for this analysis. A focus will be placed on the analysis of protein modifications. The objectives are:

1) to optimize and apply this platform to anthers and pollen tissues to establish a proteome map of developing pollen.
2) genome-scale quantification of proteins in response to temperature treatment, including establishing of thorough pre-fractionation techniques (SDS-PAGE, FPLC, HPLC or IF),
3) establishment of rapid Mass Western for specific target proteins applicable for high-throughput analysis of many plant lines,
4) integration of proteomics metabolomics and transcriptomics data (GXP,WUR,UNF) and
5) analysis of histone modifications and protein phosphorylation using proteomics profiling. The project involves plant molecular biology, biochemistry, and advanced proteomics approaches.

Where

The group of Wolfram Weckwerth, University Vienna, Department for Molecular Systems Biology, Althanstr. 14, 1090 Vienna, Austria, wolfram.weckwerth@univie.at, +43 1 427757700.

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PhD Research Project 8

Development of a gene network for modelling of pollen thermotolerance

Project description

All high-throughput approaches require the management and organization of the data produced and the integration of the manifold existing resources for the identication of variations with respect to environment or genetics. The project will include the development of an integrated database with metabolomic, transcriptomic and proteomic data associated to information related to the many gene and gene families involved. The objectives are

1) development of an efficient data management system,
2) integration of proteomics, metabolomics, and transcriptomics data derived from different experimental efforts,
3) modelling of the regulatory network implied in the HSR, and
4) comparative analysis among heat sensitive and tolerant genotypes to provide support for the functional analysis of major gene families included in the response.

The project requires data management, data mining and advanced bioinformatics.

Where

The group of Maria Luisa Chiusano, University of Naples Federico II, Department of Soil, Plants, Environmental and Animal Production Sciences, Laboratory of Computer Aided Biosciences, Via Universita 100, 80055 Portici, Italy, Chiusano@unina.it, +39 0812539492.

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