|Project Group 1 (Alexandrium minutum)|
|Allan Cemballa (Coordinator)
Linda Medlin (Coordinator)
|Alfred Wegener Institut
Am Handelshafen 12
|Project Group 2 (Pseudo-nitzschia multistriata)|
|Stazione Zoologica Anton Dohrn
|Project Group 3 (Fibrocapsa japonica)|
|Ecole Normale Superieure
Department of Biology CNRS FRE2910
|Project Group 4 (Planktothrix spec.)|
| Paul Hayes
|School of Biological Sciences
University of Bristol
Woodland Road, Bristol BS8 1UG
|Project Group 5 (Sequencing)|
| MPI for Chemical Ecology
|Project Group 6 (Sequencing, Web Page, Data Analysis)|
| Fritz Lipmann Institute for Age Research (former IMB)
Role and Contribution
The AWI will co-ordinate the ESTTAL project and will be responsible for WP1, i.e., the culture of Alexandrium minutum and Prymnesium parvum under various conditions, isolation of mRNA from these cultures, generation of cDNAs from the mRNA preparations and the ligation into a suitable vector. Vectors will be sent to Partner s 5 and 6 for transformation. Cell extracts from AWI cultures, as well as from those of Partner s 2-4, will be assayed or analysed for toxins as appropriate. EST sequences from A. minutum and P. parvum, generated by Partners 5 and 6 will be annotated at the AWI. The AWI group will participate in the annotation workshop, help in choosing appropriate genes for expression studies, and will supervise and conduct the toxin analyses. Subsequently, the AWI partner will carry out detailed expression analysis and provide expertise for microarray/chip design.
The Alfred-Wegener-Institute for Polar and Marine Research is one of 15 national research centres in Germany belonging to the Helmholz-Society. The institute, founded in 1980, is financed by the German Federal Ministry for Education, Science, Research and Technology (BMBF) and the State of Bremen. The AWI plays a major role in conducting climate and environmental research. Its official mandate requires that the institute: 1) participate in fundamental scientific research in marine regions, especially in the poles, 2) provide nation-wide co-operation of marine expeditions and related logistics and 3) contribute to international co-operative projects in polar and regional seas. The institute has four scientific departments: Benthic Ecosystems, Pelagic Ecosystems, Climate Systems and Geosystems. A data processing centre, library and three research vessels support these departments. Three major research programmes are at present underway at the AWI: 1) the study of the coupled system of the ocean-ice-atmosphere and its impact on global climate, 2) the study of living communities, and 3) the history of polar continents.
In 1995, a molecular biology working group led by Dr. L. Medlin, geared to the study of molecular ecology and phylogenetics of marine phytoplankton was established at the AWI within the Pelagic Ecosystems Department. Dr. Medlin was the first to apply the use of PCR techniques to the amplification of ribosomal RNA genes for phylogenetic use. Her working group has concentrated on the use of molecular techniques (DNA sequencing and molecular markers) to address species level questions and spatial distribution of genetic diversity in marine phytoplankton. Recent advances in the molecular group include the development of class-specific probes for dinoflagellates and species specific probes for many toxic algae and microarrays for class level probes for algal biodiversity and some toxic species. The molecular biology working group also has substantial experience in the analysis of toxin gene expression, cDNA library establishment, and EST analysis.
In 2003, Dr. Allan Cembella joined the research team at the AWI as Professor and Section Head of Marine Ecological Chemistry within the Pelagic Ecosystems Department. Dr. Cembella was leader on the project that produced the first complete sequence of the 18S rDNA gene from the dinoflagellate Alexandrium tamarense at the National Research Council, Institute for Marine Biosciences, Canada. Since then his work has focussed primarily on the physiology and genetics of toxin production and biosynthesis in marine eukaryotes. Among the emerging projects to be initiated at the AWI include determining the factors related to gene expression of toxin biosynthesis in toxigenic microalgae. An ongoing project involves the use of stable isotope labelling and integration of genomic information from EST libraries to elucidate biochemical pathways for the synthesis of the polyketide toxins known as spirolides from the marine dinoflagellate Alexandrium ostenfeldii. He is also coordinating an AWI-NRC joint project on EST libraries for A. ostenfeldii and the prymnesiophyte Chrysochromulina polylepis.
Role and Contribution
The SZN will be responsible for WP2, i.e. the growth of Pseudo-nitzschia under various conditions, isolation of mRNA from these cultures, generation of cDNAs from the mRNA preparations and the ligation into a suitable vector. Vectors will be sent to PARTNER s 5 and 6 for transformation. Samples from cultures will be sent to PARTNER 1 (AWI) for toxin assays and/or analysis as required. Pseudo-nitzschia EST sequences generated by Partners 5 and 6 will be annotated. The SZN group will participate in the annotation workshop, help in choosing appropriate genes for expression studies and will subsequently carry out detailed expression analysis. For this latter purpose, the SZN will provide expertise for microarray and chip design.
The Stazione Zoologica 'A. Dohrn' of Napoli (SZN) is a public Basic Research Institute under the supervision and control of the Italian Ministry of Scientific Research. The Institute is devoted to basic research in marine biology, developmental biology and evolution. Research is largely interdisciplinary and the Institute is committed to a policy of promoting international cooperation in scientific research. The institute comprises nine research groups: benthic ecology, biochemistry and molecular biology, biological oceanography, cell biology, ecophysiology, marine botany, molecular evolution, neurobiology, and plant molecular biology. The location of the SZN is also relevant to the goals of the project because the Bay of Naples contains a particularly diverse, seasonally changing assemblage of phytoplankton species, including Pseudo-nitzschia, one of the target taxa of the project. The SZN team has monitored this diversity on a weekly basis since the beginning of the 1980's by light microscopy. These LM data provide the information against which data produced by novel monitoring and early warning techniques can be compared.
Role and contribution
The ENS will be responsible for WP3, i.e. the growth of Fibrocapsa japonica under various conditions, isolation of mRNA from these cultures, generation of cDNAs from the mRNA preparations and the ligation into a suitable vector. Vectors will be sent to Partner s 5 and 6 for transformation. Samples from cultures will be sent to Partner 1 (AWI) for toxin measurements. F. japonica EST sequences generated by Partners 5 and 6 will be annotated. The ESN will participate in the annotation workshop and help to chose appropriate genes for expression studies. This Partner will subsequently carry out detailed expression analysis and will therefore provide expertise for microarray design.
Since 1995, Bowler's laboratory at the SZN has developed a range of molecular tools that have established the pennate diatom Phaeodactylum tricornutum as the favoured model species for dissecting diatom molecular and cellular biology. These resources include technologies for genetic transformation and for performing sexual crosses under laboratory conditions. They have also generated 12,000 ESTs from this diatom, which have been fully annotated and are accessible in a queryable database at http://avesthagen.sznbowler.com. Their work is now continuing at the Ecole Normale Supérieure in Paris, where Bowler was recently appointed director of research. The laboratory is a member of the international consortium that has annotated the complete genome sequence of the centric diatom Thalassiosira pseudonana, in a project funded by the US Dept of Energy (DOE) and coordinated the University of Washington, Seattle. Furthermore, Bowler is now coordinating the DOE-funded sequencing of the P. tricornutum, which should be completed in 2004. The group is therefore ideally suited to make an important contribution to the current project. The laboratory works alongside the team headed by Pascal Jean Lopez, who is using molecular and cellular approaches to study silica-based morphogenesis in diatoms.
Role and contribution
The University of Bristol will be responsible for the molecular biological and ecophysiological tasks in WP4, i.e. the growth of Planktothrix under various conditions, isolation of mRNA from these cultures, generation of cDNAs from the mRNA preparations and the ligation into a suitable vector. Vectors will be sent to Partners 5 and 6 for transformation. Samples from cultures will be sent to Partner 1 (AWI) for toxin assays. Planktothrix EST sequences generated by Partners 5 and 6 will be annotated. The University of Bristol group will participate in the annotation workshop, help to choose appropriate genes for expression studies and will subsequently carry out detailed expression analysis. This partner will also provide expertise for microarray/chip design.
The University of Bristol is one of the UK's top universities, with a strong tradition in research. As such, it has all of the infrastructure necessary for effective administration of externally funded research.
The School of Biological Sciences, University of Bristol has an active Microbial Ecology Research Group of which Prof. Hayes is a member. He is an experienced cyanobacteriologist with considerable expertise in gene isolation, gene characterisation and in the development and use of novel molecular genetic techniques for the analysis of population structures. Other members of the Microbial Ecology research group will contribute to the proposed project through provision of advice: three post doctoral Research Fellows (Drs Sven Becker, Katherine Evans and Patricia Sanchez Barcaldo) and one post- graduate research student (Ms. Caroline Jenkins). All individuals are currently engaged in the development and use of molecular tools for examining the genetic structure of phytoplankton and associated viral populations, including the use of Real time-PCR to monitor the expression of genes in Planktothrix. The proposed project will also make use of the skills of Mrs. Annette Richer who is vastly experienced in the maintenance of cultured cyanobacteria (over 300 strains are maintained in the Bristol culture collection). Prof. K. Edwards has wide experience in the construction and characterisation of EST libraries from cereals. Dr G. Barker is the bioinformatician within the School's genomics unit and has been responsible for the creation of bespoke EST analysis software and websites.
There is a wide pool of molecular biological expertise within the School of Biological Sciences, which hosts the University's transcriptomics unit, and elsewhere within the University. Both the School and the University encourage collaboration between research groups and across research disciplines - this helps to ensure a strong research environment. The School of Biological Sciences has all of the necessary equipment (including high-throughput sequencing and real-time PCR capability) and facilities needed to ensure the success of the relevant sections of the proposed project.
Role and contribution
The MPICE will carry out transformation of bacteria with recombinant plasmids for Partners 1-4 and will be responsible for sequencing and preliminary annotation of 50% of the ESTs in WP1- 4.
The Max Planck Institute for Chemical Ecology, Jena, was founded in 1996. It is dedicated to investigate the role of chemical signals in the interaction between living organisms, and between living organisms and their environment. In the institute, ecologists, biochemists, molecular biologists, population geneticists and organic chemists work in close collaboration to investigate and unravel the complexity of chemical communication. The institute has five scientific departments, Molecular Ecology, Bioorganic Chemistry, Biochemistry, Genetics & Evolution, and Entomology. In addition, there are two independent research groups, Biosynthesis/NMR and Mass Spectroscopy. Service groups include library, computational services, and greenhouse/plant cultivation.
Research in the Department of Genetics & Evolution is focused on elucidating the evolutionary and ecological factors that influence genetic variation within and among populations and species. Projects within the department include several EST sequencing projects on insects (10,000 ESTs for each of three species), and various genomic shotgun and BAC sequencing projects of ecologically important genomic regions from cruciferous plants.
Role and contribution
The Partner 6 will be responsible for transformation of recombinant plasmids provided by Partners 1-4, for sequencing and preliminary annotation of 50% of the ESTs in WP1- 4. This partner will also host the webpage and software tools used by all partners for annotation. All sequence data will be stored at the IMB and comparison of all data sets will be done there. The annotation workshop will be supervised.
The Institute for Molecular Biotechnology, Jena, was founded in 1992. In 2005 it was renamed to Fritz-Lipmann Institute. Several new research groups started their work in 2004. It is a member of the Science Association 'Gottfried Wilhelm Leibniz', equally financed by the German Federal Government and the state of Thuringia. The institute is a member of the Jena Centre of Bioinformatics (JCB), which focuses on Molecular communication processes in normal and pathological states. All departments work together to define and characterize new targets for drugs in infectious diseases, find molecular switches related to aging, and reveal the genomic bases for the variability in the susceptibility to age related diseases. A key role for data processing and the understanding of these phenomena plays the bioinformatics at the institute.
Research at the Department of Genome Analysis is dedicated to large scale sequencing and annotation projects, the development of software for data handling and exploitation, and disease focused genomic variability projects.
Projects within the department include sequencing and annotation of the human, rat, mouse, chimpanzee, and rhesus genomes. Several bacterial genome projects are intended to reveal the molecular basis of a complex phenotype and the variabilities within bacterial genera. In the framework of the Dictyostelium discoideum genome project the department sequences, assembles, and analysis more than 60% of the whole genome. Additionally, the department is involved in two EST projects for the characterization of gene content and expression levels in two algal species (Fragilaropsis cylindrica and Mesostigma viride).