Team:IIT Delhi/Design

Introduction

                                                                                                                                                                                                                 

Several circuits have been proposed, constructed, and implemented, leading to landmark discoveries in synthetic biology. These include systems such as the bi-stable toggle switch, and the repressilator, which brought about a paradigm shift in the field. Since then, several systems have been constructed to employ memory modules, create counters, adders, digital biosensors, and a whole wide range of other products.


Figure – A brief timeline of major notable events in the creation and development of synthetic biology (Source: Del Vecchio, Domitilla et al, Journal of The Royal Society Interface 13.120 (2016): 20160380.)

However, there are several limitations that still need to be overcome, as the field continues to make strides in every area. These involve the fact that biological systems have a lot of noises that cannot be modeled accurately to date, and the fact that metabolic burden is a major issue. Along these lines, one of the central issues is the distinct lack of digital responses in synthetic biology.
Thus, as described in the project overview, we wished to use the high cooperativity TetR homologs in such a manner so as to generate a square wave oscillator circuit. Such a system could have a whole multitude of applications; some of which were mentioned briefly in the overview, and the same are also discussed below,

Applications

                                                                                                                                                                                                                 

Generating a clock input to time biological events :

The potential of genetic clock lies in its role to triggering logic reaction for sequential biological circuits. A square wave generator could be used as a genetic clock, since square waves lie at the heart of clocks. Further, these clocks could be used in any cellular system to time particular events.

Characterising gene regulatory network nodes through impulses :

This could be used to study correlation between two genes, by coupling one of the genes to the oscillator, then observe the dynamics of the second gene. In this manner, the effect of one gene on the others could be studied.

Periodic Drug delivery - Like diabetic patients, insulin needs to be provided externally through injections or other means. Our oscillator system could be used as a patch containing bacteria that are oscillating to produce square levels of insulin to the patient once. This then would deliver insulin automatically at intervals, guided by our system .Further when the requirement for insulin would be high, the amount of insulin being delivered to them could be changed through some source which could dive a change in frequency of the oscillations (future applications could be focused on engineering frequency modulation).

Metabolic Switching – A bacterial species could be engineered to produce levels of the permease for a particular sugar in the form of a square wave. Thus, at varying intervals of time, the permease (say lac permease) would be expressed, which would cause the bacteria to start metabolizing lactose. When it goes off, the bacteria would not express the lac permease and consume glucose. In this manner, we could tune the frequency of the oscillations to ensure metabolic switching and activation of pathway shunts in the manner that we want.

Temporal Bar codes – If we can control the frequency of the oscillations and modulate the time spent by the wave in the ON and OFF state (which is basically a function of the frequency itself), we could generate a combination of 0’s and 1’s, in order to generate a bar code. This bar code would be read in time, and therefore would be a temporal bar code. A typical example of this would be to encode the word “iGEM” by 11001001, where 1 represents an ON state for say, 20 minutes. Thus, an 11 response, which represents the letter i, would then be read if the fluorescence stays on for 40 minutes. In this fashion, our device could be used for encryption of data.

For memory storage:-The system could be used as the bacterial analogue of memory storage. The base of the oscillations could be called the 0 bit, and the high point could be called the 1 bit, and these combinations of 0 and 1 bits could be used to store short term memory in biological cultures, performing the functions that the RAM (random access memory) does in computers.