Revision as of 22:00, 29 October 2008 by Philippe b (Talk | contribs)

Un petit texte pour expliquer la motivation de cette page ne serait-ce que tout simplement: On this page we report some possible uses of the FIFO device in synthetic applications.

General comment: I am not at all against an explorative, speculative section. But it's purpose must be clear very clearly focussed on the interest of the FIFO for putative applications. Discuss each time why the FIFO could be especially interesting for your application. This must be very clear in order for this section to fulfill it's purpose.

B.Artificial virus factory

We can also produce a lot of differentes kinds of self-assembly structures like virus for example,HIV: No, you can not produce... You can say (possibly)... The FIFO device provides also a circuit useful to coordinate the self-assembly of molecular structure. A possible canevas for the production of synthetic virus?

Indeed a virus such as HIV, displays ans organised sequential activation of genes that could be controled by a FIFO circuit. ARE YOU SURE OF THIS


Fig2: genetic organization of HIV virus

HIV can be produce by sequential expression of 3 genes gag,env and pol (Fig.2), those genes are be cleaved by protease P10 and then the subunits of the virus will self-assembled into mature virus. A re-enginered virus could be based on a FIFO setup where gag p10 is first expressed and Env the last (without Pol to avoid pathogenicity). In this case

  • when genes 1 and 2 are expressed, the protease P10 cleaves gag that self-assembles.
  • when 123 is expressed, Env is cleaved and self assembles with the products of gag and P10 that have already been produced.
  • finaly, when 23 is activated alone, this increases the quantity of subunits delivered from the clivage of Env. I DO NOT UNDERSTANT

In this setup I maybe understand the sequential order of activation, but I do not see why there should be the same order of inactivation. Justify please

In our case, we will expressed gag p10 and finaly Env (without Pol to avoid pathogenicity) the FIFO in this case will be essential.

If you ask us why?

For 3 main reasons :

  • First, when they genes 1 and 2 will be expressed, the protease P10 will cleave gag that will self-assemble.
  • Then, when 123 will be expressed Env will get cleaved and self assemble with the products of gag and P10.
  • Finaly, when 23 are activated alone, we will increase the quantity of subunits delivered from the clivage of Env.

Metabolic engineering of polyhydroxyalkanoate biosynthesis pathways

Human overpopulation combined with the current lifestyle urges the rational, efficient, and sustainable use of natural resources to produce environmentally friendly plastic materials such as polyhydroxyalkanoic acids (PHAs), whose production/degradation cycle reduces undesirable wastes and emissions. Our study is a new metabolic strategy to generate PHA-hyperproducer strains, that have the properties to be a sequential metabolic pathway, we believe the sequential expression may increases the production of purified PHA.

Our strategy consists on replacing the RFP,CFP and YFP genes by the PhaA ,PhaB and PhaC genes in our final system (containing oscillation,FIFO,synchronisation modules).

This strategy is more efficient than a constitutive activation for 3 main reasons:

  • First, in this application the NADPH, which is a cellular metastable fuel, is used by the PhaB to synthesize bioplastic. This molecule is very important for many metabolic pathways in bacteria. A NADPH recuperation step is then needed to ensure other metabolic activities to go on. We can then make the hypothesis that if the PhaB is always activated the bacteria will get exhausted and die quickly. In our system, the bacteria will have a NADPH recuperation step, this is why we hope bacteria will live more than in an usual chemoreactor.
  • Secondly, we hope by the order of the FIFO to make a synchronized and sequential expression in order to increase the rate of the PHA biosynthesis.
  • Third, as the quality of the bioplastic increases with time, we could predict the quality of the final product since we would know the duration of a production cycle thanks to the periodicity of our system.

Again, you cannot just state this boldly without constructing an argument.

You never explain why your system is better than simply expressing all the genes continuously at a lower level

More generally, on this whole page: We don't expect you to give very detailed projects. You just need to give simple ideas for which the interest of the FIFO seems obvious (or at least you need to try making it seem obvious). We are not so much interested in the precise mechanisms or genes involved, but rather in the principles that make your projects interesting.



  • Folding DNA to create nanoscale shapes and patterns

Paul W. K. Rothemund

  • Design of DNA origami

Paul W. K. Rothemund

  • An autonomous polymerization motor powered by DNA hybridization.

Suvir Venkataraman, Robert M. Dirks, Paul W. K. Rothemund, Erik Winfree, Niles A. Pierce.

  • Catalyzed Relaxation of a Metastable DNA Fuel.

Georg Seelig, Bernard Yurke, Erik Winfree.