[BBF Standards] question on PoPS devices

[Deepak Chandran]

Hello,

Another small inquiry about PoPS devices:

A PoPS device can only have one input and one output -- is that correct? 
If so, is it possible to create a network similar to natural regulatory 
networks (i.e. with one gene regulating multiple genes) solely through 
the use of the PoPS interface?

--Deepak

Reshma Shetty wrote:
> Hey all,
>
> A few (hopefully) clarifying comments ...
>
> On Tue, May 20, 2008 at 11:24 AM, Deepak Chandran
> <deepakc at u.washington.edu> wrote:
>   
>> A question concerning PoPS devices: do they truly resolve the cross-talk
>> problem?
>>     
>
> No.
>
> Three inverters of the same kind would interfere with one
>   
>> another, so what aspect of this particular issue does it solve? My
>> understanding was that PoPS is a way of establishing compatible
>> input/output relationships.
>>     
>
> Using PoPS as a common signal carrier resolves (in part) the issue of
> designing and building *composable* transcription-based devices.  The
> PoPS signal stanadard allows devices that either produce or receive a
> PoPS signal to be combined with other devices that produce or receive
> a PoPS signal.  (If devices are defined to produce or receive proteins
> instead, then most devices will not be composable.  See the comic for
> details.) By establishing a common signal carrier for
> transcription-based devices, we can move on to the next problem of
> ensuring that signal levels between devices are actually matched ...
> which is a whole topic in itself.  :)
>
> If there was a PoPS device that does not use
>   
>> any protein to achieve its function, then it would evade the crosstalk
>> problem; but is it possible to build a genetic network that has no
>> proteins (setting aside RNA-based transcription factors)?
>>     
>
> The crosstalk problem exists whenever you rely on molecular
> specificity in your device or system.  DNA, RNA, and protein-based
> devices could all have potential crosstalk issues.  Though, DNA- and
> RNA-only based devices are generally more amenable to rational design
> to avoid crosstalk.
>
> Just my two cents.
>
> Thanks,
>
> Reshma
>