Final Activity Report Summary - SY-STEM (Systems biology of stem cell function in arabidopsis thaliana)
General description of project goals
The scientific goal of this project was to study the morphogenetic events leading to growth and organ production in the Shoot apical meristem (SAM) of higher plants and to set up an iterative process of model building, biological testing and refinement. The SAM produces all aboveground tissues, and defines the number, type and position of lateral organs. SAMs are thus the basis of plant architecture and the determinants of major traits of agronomic importance. In view of its importance, the SAM has been extensively studied and a wealth of information is available concerning its molecular and cellular components. Nevertheless, we do not understand how these components assemble into a multicellular structure with specific shape and growth dynamics. To solve this problem, we need to develop integrative approaches, in particular using computational modelling. When the project was submitted, the interaction between biologists and computer scientists in the field was mainly limited to the data coming from sequencing projects. In particular in the plant field, there had not been a large scale, structured attempt to extend and deepen the interaction between the disciplines to other types of data (e.g. structural, biochemical,....) and to integrate the activities of computer scientists and statisticians into a full research programme. In addition it was (and still is), essential to train young scientists to become familiar with both mathematical / informatics approaches and biology.
Scientific outcomes
The project has significantly contributed to our understanding of meristem function. The results, already described in 38 publications, have shed new light on the regulatory networks controlling meristem patterning and growth, by identifying novel genes and modelling their interactions. The link between these regulatory networks and cellular responses such as cell proliferation was further characterised. The first models in the form of virtual tissues were developed, revealing unsuspected properties of the cell-cell interaction networks and suggesting new experiments. From a technical perspective, over 60 transgenic lines have been generated, and over 120 gene expression patterns have been defined using in situ hybridisation. From a more conceptual point of view, the interactions between computer scientists and biologists have clearly led to the design of novel experiments where quantitative approaches play an important role.
Training
One of the main aims of the training programmes was to ensure that all young scientists involved would acquire a clear understanding and appreciation of how biological and mathematical / informatics techniques can be effectively used in the context of an integrated research programme.
Besides the individual training, which enabled every trainee to set up an adapted training programme, the following common training program was successfully developed:
- Several courses (two - three days) on systems biology were organised. These courses were open to other members of the participant's labs and were designed for a broad public of both computer scientists (not necessarily familiar with all biological concepts) and biologists (mostly not familiar with modelling approaches).
- During the other six monthly meetings and the final workshop maximal time was given for discussion and interaction between the computer scientists and biologists. In this context poster sessions with informal discussions proved to be extremely fruitful.
- Exchanges were promoted throughout the project, which was facilitated by setting up technology platforms, where individual labs were responsible for training in specific techniques.
The scientific goal of this project was to study the morphogenetic events leading to growth and organ production in the Shoot apical meristem (SAM) of higher plants and to set up an iterative process of model building, biological testing and refinement. The SAM produces all aboveground tissues, and defines the number, type and position of lateral organs. SAMs are thus the basis of plant architecture and the determinants of major traits of agronomic importance. In view of its importance, the SAM has been extensively studied and a wealth of information is available concerning its molecular and cellular components. Nevertheless, we do not understand how these components assemble into a multicellular structure with specific shape and growth dynamics. To solve this problem, we need to develop integrative approaches, in particular using computational modelling. When the project was submitted, the interaction between biologists and computer scientists in the field was mainly limited to the data coming from sequencing projects. In particular in the plant field, there had not been a large scale, structured attempt to extend and deepen the interaction between the disciplines to other types of data (e.g. structural, biochemical,....) and to integrate the activities of computer scientists and statisticians into a full research programme. In addition it was (and still is), essential to train young scientists to become familiar with both mathematical / informatics approaches and biology.
Scientific outcomes
The project has significantly contributed to our understanding of meristem function. The results, already described in 38 publications, have shed new light on the regulatory networks controlling meristem patterning and growth, by identifying novel genes and modelling their interactions. The link between these regulatory networks and cellular responses such as cell proliferation was further characterised. The first models in the form of virtual tissues were developed, revealing unsuspected properties of the cell-cell interaction networks and suggesting new experiments. From a technical perspective, over 60 transgenic lines have been generated, and over 120 gene expression patterns have been defined using in situ hybridisation. From a more conceptual point of view, the interactions between computer scientists and biologists have clearly led to the design of novel experiments where quantitative approaches play an important role.
Training
One of the main aims of the training programmes was to ensure that all young scientists involved would acquire a clear understanding and appreciation of how biological and mathematical / informatics techniques can be effectively used in the context of an integrated research programme.
Besides the individual training, which enabled every trainee to set up an adapted training programme, the following common training program was successfully developed:
- Several courses (two - three days) on systems biology were organised. These courses were open to other members of the participant's labs and were designed for a broad public of both computer scientists (not necessarily familiar with all biological concepts) and biologists (mostly not familiar with modelling approaches).
- During the other six monthly meetings and the final workshop maximal time was given for discussion and interaction between the computer scientists and biologists. In this context poster sessions with informal discussions proved to be extremely fruitful.
- Exchanges were promoted throughout the project, which was facilitated by setting up technology platforms, where individual labs were responsible for training in specific techniques.