Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.
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Transcript of Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.
![Page 1: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/1.jpg)
1Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Solving TSP on Lab-on-a-Chip
Jiyoun Lee
![Page 2: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/2.jpg)
2Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Introduction
• TSP (Traveling Salesman Problem)– Graph with given vertexes, edges, and costs (weights)
Hamiltonian paths containing the smallest sum of costs
• Airlines, transportation
• Graph dimension– 7 vertexes, 24 edges, 5 costs
![Page 3: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/3.jpg)
3Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
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0 1 2 3 4 5 6 0 (21)
start
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0 1 6 5 4 3 2 0 (31)0 2 1 3 4 5 6 0 (27)0 2 3 4 5 6 1 0 (31)0 6 5 4 3 1 2 0 (27)0 6 5 4 3 2 1 0 (21)
![Page 4: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/4.jpg)
4Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
vertex weight(with low GC)
vertex weight(with low GC)
vertexedge edge
low melting temperature
weight
vertex weight vertex weight vertexweightweightlow melting temperature
more amplification by more denaturation
![Page 5: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/5.jpg)
5Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
ds DNA
denaturation : more denaturation of DNA strands which have less weights
primer annealing
polymerization
![Page 6: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/6.jpg)
6Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
ProcedureGenerating random paths
through the graph
Keep only those paths thatbegin with vin
Keep only those pathsthat enter exactly n vertices
Keep only those paths thatenter all of the vertices ofthe graph at least once
Separation of the solutions
Generating sequences& LIgation reaction
PCR with vin as primers
Gel electrophoresis separationby size
Affinity-purification with a biotin-avidin magnetic beads system
TGGE
Figure out the path Sequencing & readout
![Page 7: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/7.jpg)
7Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
ProcedureGenerating random paths
through the graph
Keep only those paths thatbegin with vin
Keep only those pathsthat enter exactly n vertices
Keep only those paths thatenter all of the vertices ofthe graph at least once
Separation of the solutions
Generating sequences& LIgation reaction
PCR with vin as primers
Gel electrophoresis separationby size
Affinity-purification with a biotin-avidin magnetic beads system
TGGE
Figure out the path Sequencing & readout
![Page 8: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/8.jpg)
8Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Affinity separation (7 nodes)
Ligation(Connecting each ssDNA)
PCR with Vin
Hybridization(Generating all possible paths )
Size separation by electrophoresis
Sequencing
Temperature gradient in reservoir
Isothermal reaction in reservoir
Expected problems : buffer compositionLigation bufferAffinity separation bufferCf) conventional method Purification of DNA by ethanol precipitation
Paramagnetic separationusing biotin-avidin interaction
Temperature cycling in reservoir
CE (or CGE)
![Page 9: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/9.jpg)
9Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Affinity unit
Reaction chamber for hybridizationand ligation
Reaction chamber for PCR
Electrophoresisseparation
Buffer change
Buffer changeVolume reduction?
I wish to..Eliminate the affinity stepChange the buffers in flow
![Page 10: Cell and Microbial Engineering Laboratory Solving TSP on Lab-on-a-Chip 1 Jiyoun Lee.](https://reader036.fdocuments.in/reader036/viewer/2022082518/5697bf721a28abf838c7eab2/html5/thumbnails/10.jpg)
10Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Questions and Discussions…
• Danny’s idea: addition of salts..– Not reservoir type, but channel type
• In English, please…
• Questions to Danny:– Method for inserting beads to channel.
– Channeling effect or something…
– TRIS, .. Some buffer names..
– Many beads – Yield of …