coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/reshmashettyteach... ·...
TRANSCRIPT
![Page 1: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/1.jpg)
Coming up with a project
Teach the Teachers WorkshopMay 16, 2009
![Page 2: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/2.jpg)
Talk to people
![Page 3: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/3.jpg)
Previous iGEM projectsigem.org
![Page 4: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/4.jpg)
New organisms
![Page 5: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/5.jpg)
New parts and tools for future teams
Most commonly used parts: B0015 - a terminator
F2620 - an inducible promoterB0034 - a RBS
R0011 - lac promoterPlasmid backbones
![Page 6: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/6.jpg)
Reuse and existing parts
Mechanism & Function
A transcription factor (LuxR) that is active in the presence
of a cell-cell signaling molecule (3OC6HSL) is controlled by
a regulated operator (PLtetO-1). Device input is 3OC6HSL.
Device output is PoPS from a LuxR-regulated operator. If
used in a cell containing TetR then a second input such as
aTc can be used to produce a Boolean AND function.
BBa_F26203OC6HSL PoPS Receiver
Registry of Standard Biological Parts making life better, one part at a time
License: Public
Conditions (abridged)
Output: PoPS measured via BBa_E0240
Culture: Supplemented M9, 37ºC
Plasmid: pSB3K3
Chassis: MG1655
*Equipment: PE Victor3 multi-well fluorimeter
**Equipment: BD FACScan cytometer
1E01E1
1E21E3
1E4
GFP (arbitrary units)
Doublin
gs
20
38
56
74
92
High Input (1E -7 M 3OC6HSL)
92
1E01E1
1E21E3
1E4
Doublin
gs
20
38
56
74
Low Input(0 M 3OC6HSL)
GFP (arbitrary units)
Reliability**
Genetic: >92/>56 culture doublingsPerformance: >92/>56 culture doublings
(low/high input during propagation)
Transcriptional Output Demand (low/high input)
Nucleotides: 0 / 6xNt nucleotides cell-1 s-1
Polymerases: 0 / 1.5E-1xNt RNAP cell-1
(Nt = downstream transcript length)
Chassis: MC4100, MG1655, and DH5
Plasmids: pSB3K3 and pSB1A2
Devices: E0240, E0430 and E0434
BBa_F2620 Response Time: <1 minBBa_T9002 Response Time: 6±1 minInputs: 0 M (Low), 1E-07 M (High) 3OC6HSL
Pmax: 6.6 PoPS cell-1
K: 1.5E-09 M 3OC6HSLn: 1.6
Static Performance*
Pout =Pmax [3OC6HSL]n
Kn+ [3OC6HSL]n
0E+00 1E!10 1E!09 1E!08 1E!07 1E!06 1E!05 1E!04
0
100
200
300
400
500
600
[3OC6HSL] (M)
GF
P s
yn
the
sis
ra
te (
mo
lec
ule
s c
ell!1 s!1)
Population Mean
Colony Range
Hill Equation
0
1
2
3
4
5
6
7
8
Po
PS
ce
ll!1
Part Compatibility (qualitative)
Authors: Barry Canton Ania Labno
Updated: March 2008
Sig
nalin
g D
evic
es
http://p
art
s.m
it.e
du/r
egis
try/index.p
hp/P
art
:BB
a_F
2620
BBa_F2620
R0040 B0034 C0062 B0015 R0062 PLtetO-1 RBS luxR Term. Plux,R
Component Parts
!10 0 10 20 30 40 50
0
100
200
300
400
500
600
+ 3OC6HSL
Time (min)
GF
P s
yn
thesis
rate
(m
ole
cu
les c
ell!1 s!1)
GFP synthesis rate (Low Input)
GFP synthesis rate (High Input)
Polynomial Fit (High Input)
PoPS (High Input)
0
1
2
3
4
5
6
7
8
Po
PS
cell!1
0E+00 1E!10 1E!09 1E!08 1E!07 1E!06 1E!05 1E!04
0
100
200
300
400
500
600
[AHL] (M)
GF
P s
yn
the
sis
ra
te (
mo
lec
ule
s c
ell!1 s!1)
C4HSL
C6HSL
3OC6HSL
C7HSL
C8HSL
3OC8HSL
C10
HSL
C12
HSL
0
1
2
3
4
5
6
7
8
Po
PS
ce
ll!1
Input Compatibility*
Dynamic Performance*
![Page 7: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/7.jpg)
Let the students choose
![Page 8: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/8.jpg)
Help them make smart choices
• Figure out what’s practical: How many assembly stages could the team possibly do over the course of the summer? That sets an upper limit to the size of the system.
• Design the project so that different modules can be done in parallel.
• It doesn’t have to be a brand new idea.
![Page 9: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/9.jpg)
Describe your project on your team wiki
Teach the Teachers WorkshopMay 16, 2009
![Page 10: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/10.jpg)
![Page 11: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/11.jpg)
![Page 12: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/12.jpg)
Standard assembly
Teach the Teachers WorkshopMay 16, 2009
![Page 13: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/13.jpg)
BioBrick standard parts
EcoRI XbaI SpeI PstIBioBrick part
Knight, 2003
![Page 14: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/14.jpg)
BioBrick standard assembly
E X S PBioBrick part 1 E X S PBioBrick part 2
Digest with EcoRI and SpeI
Digest with XbaI and PstI
E X SBioBrick part 1 E X S PBioBrick part 2
E X S PBioBrick part 1 BioBrick part 2Mixed
Ligate
![Page 15: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/15.jpg)
A
B
C
D
E
F
G
H
AB
CD
EF
GH
ABCD
EFGH
![Page 16: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/16.jpg)
Why use the BioBrick standard?
• It is faster to build multi-part systems
• Assembling every two parts is the same
• You can reuse parts from the Registry
• Other people can reuse your parts
• It is required to win a prize at iGEM!
![Page 17: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/17.jpg)
Get the enzymes cheaper
![Page 18: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/18.jpg)
![Page 19: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/19.jpg)
![Page 20: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/20.jpg)
![Page 21: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/21.jpg)
![Page 22: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/22.jpg)
Plasmid backbones
Teach the Teachers WorkshopMay 16, 2009
![Page 23: Coming up with a project - 2009.igem.org2009.igem.org/wiki/images/5/5d/ReshmaShettyTeach... · 5/16/2009 · New parts and tools for future teams Most commonly used parts: B0015](https://reader033.vdocuments.us/reader033/viewer/2022050520/5fa3c014d917a47273166982/html5/thumbnails/23.jpg)