1. A Realization of Information Gate by Using Enterococcus faecalis Pheromone System Kenichi Wakabayashi and Masayuki Yamamura Preliminary Proceedings of the 7 th International Meeting on DNA Based Computers (DNA7) pp. 199-207 Cho, Dong-Yeon

2. (C) 2001 SNU CSE Biointelligence Lab2 Introduction Investigations that make use of organisms  Simple computer-memory using plasmid  A single carrier by making use of gene regulation system of E. coli In vivo computing  Cells are able to be stocked up on a large scale as well as proteins and DNA.  We can construct the highly parallel devices with these materials.  Cells have many control-regulated functions that we cannot easily reproduce in vitro.

3. (C) 2001 SNU CSE Biointelligence Lab3 Organic Materials in Molecular Computing Information Carrier with Organic Materials  Cell-to-cell signal carrier with E. coli  Pheromone producing and pheromone receiving cells  It can produce luminescence protein only when two types of cells exist together. Pheromone-induced Conjugation of Enterococcus faecalis  Enterococcus faecalis and their pheromones induce conjugative plasmid transfer.  There are a few pheromone inhibitors secreted by male E. faecalis.

4. (C) 2001 SNU CSE Biointelligence Lab4

5. 5 Design of E. faecalis Information Gate We can regard pheromone and plasmid as a kind of INPUT and OUTPUT.  Entry of INPUT signal A and B into the information gate.  Data processing by E. faecalis pheromone system.  Discharging of OUTPUT signal X from the information gate.

6. (C) 2001 SNU CSE Biointelligence Lab6 Realization Plan of Information Gate Outlines of Experimental Procedure  Input signals are virtually expressed by a combination of two pheromone inhibitors.

7. (C) 2001 SNU CSE Biointelligence Lab7  Model of E. faecalis information gate

8. (C) 2001 SNU CSE Biointelligence Lab8 Experimental Confirmation of Information Gate  Four transfer-plasmids that contain antibiotic resistance genes as a marker  We will test if the entire procedure is correctly done by addition of antibiotic substances.  If specificity of conjugation manner is enough, recipients can survive under presence of only one class of antibiotic substance.

9. (C) 2001 SNU CSE Biointelligence Lab9 Discussions Features of E. faecalis information gate  Variety of conjugative plasmid  There are up to 20 classes of conjugative plasmid.  More complicated system may be able to construct with designing with additional a few plasmid.  Sensitivity to pheromones  Transferability  Kinetics  Entire reaction of E. faecalis information gate is comparably slow.  Other aspects  Conjugation system of E. faecalis is inducible by pheromone, includes homogenous conjugation, and carries highly aggregates.

10. (C) 2001 SNU CSE Biointelligence Lab10 Cascading of Information Gate  E. faecalis information gate is able to be piled up if we design plasmids so as to produce certain classes of pheromone inhibitors.  We can set I3 and I4 inhibitor genes in p1 plasmid: OUTPUT signal ‘A=0’  We can set signal freely in every four plasmids.  For example, we can set output signals {0, 0, 0, 1} in the four plasmids {p1, p2, p3, p4}  AND operation  We can manage all types of Boolean operation and freely accumulate them. Scale of Information Gate – Future Work

11. (C) 2001 SNU CSE Biointelligence Lab11 Conclusions This paper introduces an information gate by using E. faecalis pheromone system. E. faecalis information gate brings a different new look in molecular computing. E. faecalis has experimentally some difficulties.