LMB562

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Contents

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
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  2. Error fetching PMID 16711359: [SciAm1]
  3. Error fetching PMID 18724274: [Embo]
All Medline abstracts: PubMed HubMed
Landmarks
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  1. Error fetching PMID 10659857: [Toggle]
  2. Error fetching PMID 10659856: [Repress]
  3. Error fetching PMID 16306980: [Voigt]
  4. Error fetching PMID 16306982: [Elo]
  5. Error fetching PMID 15858574: [Weiss]
  6. Error fetching PMID 16612385: [Keas]
All Medline abstracts: PubMed HubMed
Selected from external links
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  1. Error fetching PMID 20689598: [hongjae]
  2. Error fetching PMID 19749742: [areum]
  3. Error fetching PMID 20485551: [jihee]
  4. Error fetching PMID 15875027: [babu]
  5. Error fetching PMID 20488990: [woochang]
  6. Error fetching PMID 21246151: [Hyeokjin]
  7. Error fetching PMID 23066081: [saeyoung]
  8. Orth JD, Thiele I, Palsson BØ. What is flux balance analysis?. Nat Biotechnol. 2010 Mar;28(3):245-8. PMID: 20212490

    [byoungnam]

All Medline abstracts: PubMed HubMed
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  2. Error fetching PMID 16330045: [jihee20]
  3. Error fetching PMID 22911685: [hongjae18]
  4. Error fetching PMID 22983089: [woochang22]
  5. Error fetching PMID 22442681: [hanseong23]
  6. 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]

All Medline abstracts: PubMed HubMed
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  1. Error fetching PMID 18644449: [seayoung25]
  2. Error fetching PMID 19633652: [hyeokjin26]
  3. Error fetching PMID 18410688: [byoungnam27]
All Medline abstracts: PubMed HubMed

Practice with R package

Preparation
  1. install R package
  2. install required library package
how to install packages
>install.pacakages("deSolve")
Repressilater
Repress.png
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
Genetictoggle.png
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
Nature WEB focus
Science
PubMed database
Google scholar

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?
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