New Design

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Parts Table from MWSU
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Modeling Random Pancake Flipping
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Modeling 8 Stacks of 2 Pancakes
( 1 2) (-1 2) ( 1 -2) (-1 -2)
( 2 1) (-2 1) ( 2 -1) (-2 -1)
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Modeling 8 Stacks of 2 Pancakes
Solution is (1, 2) or (-2, -1)

• ( 1, 2)
• (-2, -1)

( 1, -2) (-1, 2) (-2, 1) ( 2, -1)
(-1, -2) ( 2, 1)
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Modeling 8 Stacks of 2 Pancakes
Solution is (1, 2) or (-2, -1)

• ( 1, 2)
• (-2, -1)

( 1, -2) (-1, 2) (-2, 1) ( 2, -1)
(-1, -2) ( 2, 1)
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Modeling 384 Stacks of 4 Pancakes
2n (n!) X Combinations 24 (4!) 384
Combinations
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Modeling 384 Stacks of 4 Pancakes


Build one representative of each family




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Define a Biological Pancake
Tet
Nonfunctional
RBS
RE
hixC
pBad
hixC
hixC
pancake 1
pancake 2
Tet
Functional
RBS
RE
pBad
hixC
hixC
hixC
pancake 1
pancake 2
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One Pancake Constructs
PredictedTet Resistance
Observed Tet Resistance
(1) 2


(-1) 2
-

1 (2)


1 (-2)
-

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Detect Flipping via Restriction Digest
NheI
NheI
ExpectedFragment Size
(1) 2
200 bp
(-1) 2
300 bp
1 (2)
200 bp
1 (-2)
1100 bp
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Hin-mediated Flipping
Tet Pancake Flipping
pBad Pancake Flipping
1 (2) Hin
(1) 2 Hin
1 (-2)
(-1) 2
1 (2)
(1) 2
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Read-Through Blocked by pSB1A7
Observed Tet Resistancein pSB1A3 (1) 2
(-1) 2 1 (2) 1 (-2)
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Read-Through Blocked by pSB1A7
Observed Tet Resistancein pSB1A3 (1) 2
(-1) 2 1 (2) 1 (-2)
Observed Tet Resistancein pSB1A7 (1) 2 -
(-1) 2 1 (2) - 1 (-2)
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Original Design Problems
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Original Design Problems
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Original Design Problems
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Two-Plasmid Solution

• 1 Two pancakes (Amp vector)
• 2 AraC/Hin generator (Kan vector)

Tet
RBS
pSB1A7
hixC
hixC
hixC
pBad
AraC PC
Hin LVA
RBS
pSB1K3
pLac
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Biological Equivalence Problem
(1,2)
LB Amp Kan Tet
(-2,-1)
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Biological Equivalence Solution
(1,2)
(1,2)
LB Amp Kan Tet
(-2,-1)
(-2,-1)
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Eight Two-Pancake Stacks
(2,1)
(1,2)
(2,-1)
(1,-2)
(-1,2)
(-2,1)
(-1,-2)
(-2,-1)
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Results
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CONCLUSIONSConsequences of DNA Flipping Devices
-1,2 ? -2,-1 in 2 flips!
PRACTICAL Proof-of-concept for bacterial
computers Data storage n units gives 2n(n!)
combinations BASIC BIOLOGY RESEARCH Improved
transgenes in vivo Evolutionary insights
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Next Steps
Better control of kinetics Slow down Hin
activity Determine x flip seconds-1 Size
bias? Improved insulating vector Accepts
B0015 double terminator Bigger pancake
stacks
Number of flips vs.Time?
Number of flips
Time
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Summary What We Learned
Multiple campuses increase capacity with
parallel processing Collective
Troubleshooting Size does not matter (College
vs. University)
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Summary What We Learned
Math and Biology mesh really well Math
modelingWe proved a new theorem! Challenges of
biological components
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But above all
We had a flippin good time!!!
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Extra Slides gtgtgt
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Modeling Random Flipping
for trial 1 to n trials stack
input_stack flips 0 while stack
1k flips flips 1 int choose_random_interv
al stack stack(1(int(1)-1)) -1
fliplr(stack(int(1)int(2)))
stack(int(2)1k) end end
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Flip length 1
Flip length 2
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Modeling 384 Stacks of 4 Pancakes
10 combinations 1 flip from solution 10 chance
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Effect of Plasmid Copy Number
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