Final Report Summary - FISH & CHIPS (Towards DNA chip technology as a standard analytical tool for the identification of marine organisms in biodiversity and ecosystem science)
Loss of biodiversity in the marine environment due to human activities is one of the major threats for sustainable development, which is a primary European Union goal. The FISHANDCHIPS project aimed to develop deoxyribonucleic acid (DNA) chips for the identification of marine organisms in European seas as a cost effective, reliable and efficient technology in marine biodiversity and ecosystem research, given that classical microscopy methods were extremely time consuming and required a high degree of taxonomic expertise.
The project demonstrated that DNA chips could be utilised for the identification of marine animals and phytoplankton, therefore facilitating research on dispersal of ichthyoplankton, monitoring of phytoplankton and identification of bioindicators as well as prey in gut contents analysis. A combined biological and technical approach was implemented for the project goals accomplishment. The biological material was sampled by marine biologists and suitable molecular markers, consisting of mitochondrial and nuclear genes, were sequenced for probe design via construction of gene probe libraries and determination of their specificity. Particular attention was given on the involvement of Small and medium enterprises (SMEs) in order to strengthen their competitiveness and foster their leading roles in the European market. In addition, an online database was established to allow for data exchange between the involved parties.
The first version of the developed fish chips was tested for specificity in silico against background species. The second version was similarly tested and showed very specific binding to the corresponding probe. Furthermore, probes which were designed based on cytochrome oxidase I (COI) sequences were tested in hybridisation experiments. Interestingly, the number of mismatches was not related to the specificity of the hybridisation signal, while probes of equal length exhibited different hybridisation efficiencies. The latter was possibly explained by the distance between the probe binding site and the labelled end of the target DNA. The detection and discrimination limits of the fish chip were being further investigated by the time of the project completion. The mitochondrial COI gene from five invertebrate species was also employed for the design of capture oligonucleotides, for which very promising results were obtained through testing. In addition, the project developed molecular probes with great potential for distinguishing species, or even clades, of harmful algae blooms (HABs).
The results obtained for the developed DNA microarrays demonstrated that the implemented approach was seemingly feasible and suitable for the genetic identification of marine organisms. Reliability under routine application was still under investigation by the time of the project completion. Nevertheless, this project was the first application of DNA microarray technology for the identification of fishes and benthic invertebrates and it was therefore anticipated that it would encourage more research groups towards the use of the method for the identification of marine organisms as part of ecological research.
The project demonstrated that DNA chips could be utilised for the identification of marine animals and phytoplankton, therefore facilitating research on dispersal of ichthyoplankton, monitoring of phytoplankton and identification of bioindicators as well as prey in gut contents analysis. A combined biological and technical approach was implemented for the project goals accomplishment. The biological material was sampled by marine biologists and suitable molecular markers, consisting of mitochondrial and nuclear genes, were sequenced for probe design via construction of gene probe libraries and determination of their specificity. Particular attention was given on the involvement of Small and medium enterprises (SMEs) in order to strengthen their competitiveness and foster their leading roles in the European market. In addition, an online database was established to allow for data exchange between the involved parties.
The first version of the developed fish chips was tested for specificity in silico against background species. The second version was similarly tested and showed very specific binding to the corresponding probe. Furthermore, probes which were designed based on cytochrome oxidase I (COI) sequences were tested in hybridisation experiments. Interestingly, the number of mismatches was not related to the specificity of the hybridisation signal, while probes of equal length exhibited different hybridisation efficiencies. The latter was possibly explained by the distance between the probe binding site and the labelled end of the target DNA. The detection and discrimination limits of the fish chip were being further investigated by the time of the project completion. The mitochondrial COI gene from five invertebrate species was also employed for the design of capture oligonucleotides, for which very promising results were obtained through testing. In addition, the project developed molecular probes with great potential for distinguishing species, or even clades, of harmful algae blooms (HABs).
The results obtained for the developed DNA microarrays demonstrated that the implemented approach was seemingly feasible and suitable for the genetic identification of marine organisms. Reliability under routine application was still under investigation by the time of the project completion. Nevertheless, this project was the first application of DNA microarray technology for the identification of fishes and benthic invertebrates and it was therefore anticipated that it would encourage more research groups towards the use of the method for the identification of marine organisms as part of ecological research.