Team:Heidelberg/Project Highlights

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= Project Highlights =


 * We are able to predict functional mammalian promoter sequences
 * We have created a functional biochemical synthesis method for the generation of promoters libraries
 * We have developed novel standards for measurement of promoters in mammalian cells
 * 4 RFCs, well characterized parts

We are able to predict functional mammalian promoter sequences
We created HEARTBEAT, a model portfolio based upon genome-wide bioinformatic analysis and fuzzy logic. We used these tools to predict promoter sequences and subsequently synthesized those sequences. We found that promoters most closely matching the model predictions work, whereas others do not (Fig 1). Read more about these results on the "HEARTBEAT database" page. We also present a GUI which enables the users to design the promoter of their needs.

We have created a functional biochemical synthesis method for the generation of promoters libraries
We developed RA-PCR, a biochemical method for the generation of randomized promoter libraries (Fig. 2). Using this method we created a library of constitutive promoters (Fig. 3), an NF-&kappa;B responsive promoter which was subjected to extensive characterization (Fig. 4) as well as some other regulated promoters.



We have developed novel standards for measurement of promoters in mammalian cells
Applying both qRT-PCR and flow cytometry, we developed two new relative units in analogy to bacterial RPU for use in mammalians: Relative Expression Units (Fig. 5) and Relative Mammalian Promoter Units (Fig. 6). We applied these units to the characterization of our promoters, as well as an existing promoter from the registry. Read more about our Measurement subproject...

4 RFCs, well characterized parts
According to the standards required by synthetic biology we submitted all the methods and units we developed as RFCs (Request for Comments). By introducing new standards for synthetic biology in mammalian cells, we hope to initiate a process that will allow the number of mammalian parts in the registry to skyrocket within the next years:
 * RCF 41: Units for Promoter Measurement in Mammalian Cells
 * RFC 42: RA-PCR, a method for the generation of randomized promoter libraries
 * [[Media:RFC_43-design.pdf|RFC 43]]: Design of specific mammalian promoters by in silico prediction
 * RFC 45: Cloning Standard for Mammalian BioBrick Parts and Devices

We also submit more than 10 well-characterized parts to the registry (see Parts Characterization). Also, we submit several other parts, for which we offer at least a rough characterization (Find our full parts list here)


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