Objective
DNA analysis will become an important clinical tool in identification the composition of microbial species living in the gut. The most dominant technique at the time is based on PCR amplification of the 16s rDNA gene and subsequent sequencing of the variable region in the gene. This method however is limited in the amount of detail it provides and is notoriously susceptible to primer bias. Furthermore, due to the requirement of a PCR machine and sequencer the technique is too expensive and time consuming for a clinical setting.
Over the past few years nanopores have been heralded as a cheap alternative for biomolecular analysis. Specifically solid-state nanopores, which consist of a small pore in a solid membrane, have the potential for cost-effective mass-production in cleanroom facilities. Furthermore, since these pores can detect double stranded DNA they can easily be used for analysis of DNA maps.
In this proposal I suggest to use DNA mapping with solid state nanopores. The basic idea is to sequence-specifically label DNA molecules using DNA Methyltransferases and synthetic analogues of the natural cofactor S-adenosyl-methionine. The pattern of labels attached to the DNA is unique for the underlying sequence.
In my Ph.D. I used this method to transfer fluorescent dyes to the DNA and subsequently extracted the DNA map using super resolution fluorescence microscopy. In this case, the attached label will induce a current-drop when the DNA molecule translocates through the channel. The extracted current-trace will then be converted to a DNA map in basepairs and can be used to match to a real sequence. This proposed method can be used to identify genomic elements and eventually be used to recognize species, for a fraction of the cost of 16s rDNA sequencing.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences genetics DNA
- natural sciences physical sciences optics microscopy
- natural sciences biological sciences microbiology
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Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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H2020-EU.1.3. - EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions
MAIN PROGRAMME
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H2020-EU.1.3.2. - Nurturing excellence by means of cross-border and cross-sector mobility
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Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
MSCA-IF-EF-ST - Standard EF
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Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) H2020-MSCA-IF-2016
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Net EU financial contribution. The sum of money that the participant receives, deducted by the EU contribution to its linked third party. It considers the distribution of the EU financial contribution between direct beneficiaries of the project and other types of participants, like third-party participants.
1015 LAUSANNE
Switzerland
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.