LMB562

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Revision as of 02:56, 22 October 2012

Class Description

This is introductory class to cover topics in synthetic biology by its past (origin), present and future.

The course can be divided into three sessions

1. Fundamental principles of synthetic biology
2. Landmark papers in synthetic biology
3. Current topics and future direction

Additional topics - ethical issues and risks in synthetic biology

1. iGEM
2. DIYBio

Presentation schedule

9/10 Hongjae (RM1), Jeehee (RM2), Areum (RM3)

• Reading report
  • Reading 1 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Jeehee
  • Reading 2 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang
  • Reading 3 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Jeehee

9/17 No class - 2012 IBS (Daegu) symposium

9/24 Babu (RM4), Woochang (RM5), Byungho (RM6)

• Reading report
  • Reading 4 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Jeehee, Byungho, Hongjae, Babu
  • Reading 5 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Byungho, Hongjae, Jeehee
  • Reading 6 - Hanseong, Hyeok-Jin, Byungnam, Saeyoung, Woo-chang, Hongjae, Jeehee, Babu

10/1 No class - August Full Moon (Holiday)

10/8 No class - iGEM 2012 (Hong Kong)

10/15 Self study (R code)

10/22 Hyeokjin, Saeyoung, Byungnam

10/29 Hongjae, Areum, Jeehee

11/5 Babu, Woochang, Byungho

11/12 Hyeokjin, Saeyoung, Byungnam

11/19 Hongjae, Areum, Jeehee

11/26 Babu, Woochang, Byungho

12/3 Hyeokjin, Saeyoung, Byungnam

12/10 Final exam

Course materials

Fundamental principles

1. Error fetching PMID 16306983: [DrewEndy1]
2. Error fetching PMID 16711359: [SciAm1]
3. Error fetching PMID 18724274: [Embo]

Landmarks

4. Error fetching PMID 10659857: [Toggle]
5. Error fetching PMID 10659856: [Repress]
6. Error fetching PMID 16306980: [Voigt]
7. Error fetching PMID 16306982: [Elo]
8. Error fetching PMID 15858574: [Weiss]
9. Error fetching PMID 16612385: [Keas]
10. Error fetching PMID 16330045: [Chris]

Practice with R package

Preparation

1. install R package
2. install required library package

how to install packages

>install.pacakages("deSolve")

Repressilater

R-code

library(deSolve)
### Repressilator
### Elowitz & Leibler (2000)
repress = function(t,y,p) {
  dy = rep(0,6);
  dy[1] = -y[1] + p[1]/(1.+y[4]^p[4])+p[2];
  # dy[1] lacI; dy[4] CI
  dy[2] = -y[2] + p[1]/(1.+y[5]^p[4])+p[2];
  # dy[2] tetR; dy[5] LacI
  dy[3] = -y[3] + p[1]/(1.+y[6]^p[4])+p[2];
  # dy[3] cI; dy[6] TetR
  dy[4] = -p[3]*(y[4]-y[3]); # cI
  dy[5] = -p[3]*(y[5]-y[1]); # lacI
  dy[6] = -p[3]*(y[6]-y[2]); # tetR
  return(list(dy))
  # p[1..4] = c(alpha,alpha0,beta,hill)
}
# initial parameters
x0 = 2*runif(6); p = c(50,0,.2,2); t = seq(0,500,by=0.1)
out = lsoda(x0,t,repress,p)
matplot(out[,1],out[,2:4],type="l")

Genetic toggle switch

R-code

### Genetic toggle switch
### Gardner & Collins (2000)
Toggle=function(t,y,parms) {
  u=y[1]; v=y[2];
  du= -u + parms[1]/(1+v^parms[2]);
  dv= -v + parms[1]/(1+u^parms[3]);
  dY=c(du,dv);
  return(list(dY));
}

x0=c(.2,.1); times=seq(0,50,by=0.2)
out=lsoda(x0,times,Toggle,parms=c(3,2,2))
matplot(out[,1],out[,2:3],type="l",ylim=c(0,3),xlab="time t",ylab="u,v");
# phase portrait
plot(out[,2],out[,3],type="l",xlab="u",ylab="v")

External links

PLoS collections

• PLoS ONE organized Synthetic Biology Collections

Nature WEB focus

• Synthetic systems biology

Science

• Special issue for synthetic biology

PubMed database

• synthetic biology - search results

Google scholar

• synthetic biology - search results

Open questions

1. What is 'synthetic biology'?
2. How is synthetic biology different with traditional genetic engineering?