Tasks

The Work Package Structure Overview

WP Title WP leader
1 Scientific and technical fundamentals
   Subprojects 1&2
R. Schweyen
(U. Vienna)
2 Data acquisition
   Subprojects 1-6
J. Arino
(UAB)
3 In silico modelling
   Subprojects 1-4
E. Klipp
(MPIMB)
4 Data- and material banks
   Subprojects 1&2
J. Ludwig
(U. Bonn)
5 Project management 
   Subprojects 1&2
J. Arino
(UAB)
work package structure

Work Packages Goals

In work package 1,

a horizontal activity the main goal is to agree on and standardise (subproject 1 - standardisation) as much experimental conditions as possible. These comprise but are not limited to one common S. cerevisiae genetic background, one standard growth condition for wild type and knock outs and standardised stress conditions (salt, pH, osmotic stress) and a standardised description of growth phenotypes. All collected information (each known involved gene and its corresponding knock out growth phenotype under the defined normal and stress conditions, biochemical data) will be organised and formatted (subproject 2) in order to i) identify on large scale information or knock-out gaps that must be addressed in further experimental work and ii) and provide the format and input for the database development (WP4) and modelling (WP3). It is expected that this subproject serves to primarily identify the gaps, that is, what is not known about en route of/for an individual transporter/ion. Thereby combined efforts can be efficiently directed to close the gaps and enhance the picture.

         

In work package 2

the main goal is the entire experimental work necessary to comprehensively analyse alkali-metal and selected divalent cation transporting, signalling and responding factors. This will comprise approaches to identify potential new genes as well as investigations of transcription levels (subproject 1) under the defined conditions, including construction of specific single or combinatorial knock-outs (within common agreed genetic background), metabolic (subproject 2) and proteome profiling (subproject 3), involving e.g. functional and post transnational modification analysis. Subproject 4 addresses the construction of a GFP expression library, intended to provide time resolved protein concentrations under the defined conditions that can also be used for the subcellular localisation of involved, but yet not clearly localised proteins (if necessary in conjunction with other or organelle marker fluorophore tags). Downstream elements of the stress signalling cascade, such as 14-3-3 proteins will be analysed within subproject 5. In subproject 6 the transcriptional responses to unphysiological external Mg2+ concentrations and to K+ overload of mitochondria will be explored. All obtained data will be provided in formats that enables straight input to WP3. 

        

In work package 3

the final goal is to model cation homeostasis in yeast and, as such, central to the project. Here all input from the matrix subproject, the transcriptome and proteome subprojects, etc. will create the input for mathematical modelling The aim of this WP is to develop a global understanding of the cation network of yeast at the system biological level. That means experiments shall be performed that produce data, which are suitable for developing appropriate mathematical models. Finally, these models will provide an in silico representation of the synthesis, maintenance and regulation of the cellular cation network (including all relevant proteins). Such a model will provide a deeper understanding of the design principle employed by nature, but it allows also studying interesting questions that are related to practical applications and problems. It will, for instance, be possible to investigate the effects and mechanisms of cation transporter diseases that also occur in higher organisms. The model will help to identify critical components of the regulation network that might be interesting targets for future pharmacological intervention. Similarly, the dynamic model will also allow to study the causes of heavy metal induced toxicity on the cellular metabolism. In addition, due to the complexity and intrinsic heterogeneity of the data produced by WP2 it is advisable to define a Pattern Recognition unit (Subproject 4) that would join complementary expertises of different partners.

       

Work package 4

comprises three horizontal activities that are data- (subproject 1) and material banks (subproject 2) and a conceptual framework. The database will be constructed on the basis of WP1 results (on existing data and information) in order to provide as much formatted and searchable information as possible for the experimental work in WP 2 and the theoretical work in WP3. During project run time the data base will be maintained and updated according to the results of work package 3, subproject 1. To ensure the consortium group’s continuous information the data base will be accessible via the TRANSLUCENT database homepage (consortium restricted use). This will result in a conceptual framework by generating from the experimental and theoretical results overviews for individual cation transport, signalling, regulation and modification routes (complementary to WP3). Information from WP1 (subproject 2) will be used to construct first pictures and overviews, consecutively during project run time results from WPs2 and 3 will be added. The material bank (WP4, subproject 2) is intended as decentralised information point and PC based repository about all available strains, mutants, plasmids, constructs within the consortium. The material bank serves during project run time as service unit to all consortium members and may later be publicly available.  

      

Work package 5

comprises the horizontal project management activities. Two subprojects address the necessities as described above including homepage development and maintenance.