LMB562

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Latest revision as of 07:19, 4 December 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, Byoungnam, Saeyoung, Woo-chang, Jeehee

Reading 2 - Hanseong, Hyeok-Jin, Byoungnam, Saeyoung, Woo-chang

Reading 3 - Hanseong, Hyeok-Jin, Byoungnam, 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, Byoungnam, Saeyoung, Woo-chang, Jeehee, Byungho, Hongjae, Babu

Reading 5 - Hanseong, Hyeok-Jin, Byoungnam, Saeyoung, Byungho, Hongjae, Jeehee

Reading 6 - Hanseong, Hyeok-Jin, Byoungnam, 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 (RM7), Saeyoung (RM9), Byungnam (RM8)

Reading report

Reading 7 - Byoungnam, Woo-chang, Hongjae, Areum, Babu

Reading 8 - Hyeok-Jin, Woo-chang, Hongjae, Areum, Babu

Reading 9 - Hyeok-Jin, Byungnam, Woo-chang, Hongjae, Areum, Babu

10/29 Hongjae (RM10), Areum (RM11), Jeehee (RM12)

Reading report

Reading 10 - Woo-chang, Hyeokjin, Babu, Areum, Byoungnam, Byoungho

Reading 11 - Woo-chang, Byoungho, Babu, Saeyoung, Hongjae, Byoungnam, Hyeokjin, Jihee

Reading 12 - Woo-chang, Hyeokjin, Jihee, Babu, Byoungho, Saeyoung, Areum, Byoungnam

11/5 Babu (RM13), Woochang (RM14)

Reading 13 - Woo-chang, Babu, Saeyoung, Hongjae, Byoungnam, Hyeokjin, Jihee, Hongjae, Areum

Reading 14 - Woo-chang, Babu, Saeyoung, Hongjae, Byoungnam, Hyeokjin, Jihee, Hongjae, Areum

11/12 Hyeokjin (RM15), Saeyoung (RM16), Byungnam (RM17)

Reading 15 - Woo-chang, Babu, Hongjae, Byoungnam, Jihee, Areum

Reading 16 - Woo-chang, Babu, Hongjae, Jihee

Reading 17 - Woo-chang, Babu, Hongjae, Areum

11/19 Hongjae (RM18), Areum (RM19), Jeehee (RM20)

Reading 18 - Woo-chang, Babu, Areum, Byoungnam

Reading 19 - Woo-chang, Babu, Areum, Byoungnam, Hongjae

Reading 20 - Woo-chang, Babu, Areum, Byoungnam, Hongjae

11/26 Babu, Woochang, Hanseong

Reading 21 - Jihee, Woo-chang, Babu, Byoungnam

Reading 22 - Jihee, Babu, Byoungnam, Areum

Reading 23 - Babu, Byoungnam, Areum, Woochang

12/3 Hyeokjin,Saeyoung, Byungnam

Reading 24 - Babu, Hongjae, Woo-chang, Areum

Reading 25 - Babu, Hongjae, Woo-chang, Areum, Byoungho

Reading 26 - Babu, Hongjae, Woo-chang, Areum, Byoungho

12/10 Final exam

Reading materials (RMs)

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]

Selected from external links

10. Error fetching PMID 20689598: [hongjae]
11. Error fetching PMID 19749742: [areum]
12. Error fetching PMID 20485551: [jihee]
13. Error fetching PMID 15875027: [babu]
14. Error fetching PMID 20488990: [woochang]
15. Error fetching PMID 21246151: [Hyeokjin]
16. Error fetching PMID 23066081: [saeyoung]
17. Orth JD, Thiele I, Palsson BØ. What is flux balance analysis?. Nat Biotechnol. 2010 Mar;28(3):245-8. PMID: 20212490 [byoungnam]

18. Error fetching PMID 22132112: [areum19]
19. Error fetching PMID 16330045: [jihee20]
20. Error fetching PMID 22911685: [hongjae18]
21. Error fetching PMID 22983089: [woochang22]
22. Error fetching PMID 22442681: [hanseong23]
23. Mondragón-Palomino O, Danino T, Selimkhanov J, Tsimring L, Hasty J.Entrainment of a population of synthetic genetic oscillators.Science. 2011 Sep 2;333(6047):1315-9.PMID: 21885786 [babu24]

24. Error fetching PMID 18644449: [seayoung25]
25. Error fetching PMID 19633652: [hyeokjin26]
26. Error fetching PMID 18410688: [byoungnam27]

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

Definition

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

Model

1. What is the Hill equation (Hill model)? How is it different with the Michaelis-Menten equation?
2. What is the relevance of those models and analysis in biological systems?

Floquet analysis?

Hopf bifurcation analysis?