Members: (Add Your Name if interest post cutoff)
Erik Ersland
Shinjini Saha
Jiaqi Xie
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Just setting a page down to see what you guys have and to share resources.
Linked list circuit
if you add a timer to produce the advance signal, it will be a clock
This uses only cas9 repressors and a small molecule signal to handle states.
Key:
-> constitutively active promoter
n:binding site for cas-9 repressor for nth node, allows transcription without cas9
n':binding site for cas-9 repressor for nth node, allows transcription without cas9
A: (code for advance) some system so that A must be present for transcription
(n) and (n'): codes for guide rna that binds to n or n' to stop transcription there
payload: the reporter for a node, each node will have a different one so you can see state, each node will probably have a different fluorescent protein.
, breaks up units of transcription regulators and gene expression, each unit between commas is a promoter, the appropriate regulators, and the expressed molecule
each line is a node
circuit of nodes (there isn't supposed to be a cross out, I don't know why its there)
->0'(1),0 payload,>0(3'),>0(3),->A0(0')
->1'(2),1 payload,>1(0'),>1(0),->A1(1')
->2'(3),2 payload,>2(1'),>2(1),->A2(2')
->3'(0),3 payload,>3(2'),>3(2),->A3(3')
explanation of components (same comma convention):
normally blocks next node,payload is on when node active, previous nodes blocking blocked when node active so a node activates itself, node blocks previous node for state transitions, node blocks blocking of next node when active and activator present which causes next node to turn on also for state transitions.
initial state: [(0),(1),(2),(3)] present (blocking active behaviour)
all nodes are now inactive and [(0),(1),(2),(3)] produced
state change: (0') introduced
(1) stops being produced by node 0
1 becomes active
1 payload expressed
(0') produced, reinforcing 1 on state
[(0),(2),(3),(0')] present
state is now 1 and only one active
state change: (A) introduced ,now [(0),(2),(3),(0'),(A)] present
0,2,3 ignore it because normal suppressors active
on node 1, (1') is produced since (1) not present and (A) present ,now [(0),(2),(3),(0'),(A),(1')] present
(2) not produced any more, now [(0),(3),(0'),(1')] present
(you need to remove (A) before 2 fully active since it would cause another state transition, may also get around this by using two different (A)'s and alternating between them as well since the one that causes 1 to 2 would note cause 2 to 3, other mechanisms probably exist as well)
2 becomes active
2 payload expressed
(1') produced, enforcing 2 on state
(1) produced, deactivating 1 (the intermediate state of 1 and 2 both active automatically proceeds forwards to just 2 being active)
(0') not produced
now [(0),(1),(3),(1')] present
state is now 2 and only 2 active
future state changes: each addition of (A) will move state forward one slot
for an active stage n, (A) causes n+1 to be active, so both n and n+1 are active, then n+1 causes n to be inactive, so n+1 is the only active state.
all nodes are inactivated by the previous node except the active one.
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14 Feb 9
Applications:
Time progression, biological clock.
Any multi-step chemical/biological process moderated by a single organism.Beer brewing.
Ethanol/Biofuel production.
Drugs/Enzyme production.
Chemical processes with steps that would normally interfere with one another moderated locally.
Safety precaution, self-termination.
Biological CS circuits. Large AND and OR Gates
Add back command to create Turing Machine.
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Implementation:
Cas9, Guide RNA for repression.
mRNA sensing repression.
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14 Feb 12
Updated Powerpoint with improved sprites and arrow pushing. V2
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14 Feb 13
Brainstorming session.
Forgot some repression arrows. Message was clear enough such that no one cared. Will fix if not lazy. -JX
Cell that allows for post processing.Yeast that has the capability to creating a variety of beer.
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14 Feb 20
Victory.
Our brave soldiers have triumphed over the forces of ??? in the battle of the first cutoff.
Todo: Make a mailing list and post on wiki and igem-2014.
Coordinate meeting times for preliminary experiments and circuit design.
Human(e) practices?
Monsanto?
Control? Termination? Transfer?
- JX
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14 Feb 27
Pre-meeting Pow Wow:
Anschluss failed. 
Signalling unit.
Middle segment can be one piece or separate, need testing.
Activating small molecule:
rtTA (Tet-ON) system:
http://www.tetsystems.com/science-technology/scientific-figures/#c22 (first diagram to the right.)
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Testing:
Primary Chassis Considered: Yeast
Middle segment can be one piece or separate, optimization?
Precise mechanism for the AND of the last part needs testing.
(NOT A) && B Gate
Degradation rate of Repressors, measured and controlled. State change time sensitive.
Look up circuitry. 6.004 ocw materials.
Propagation times and state thresholds (determined by cooperativity and binding kinetics, and etc. ).
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Motivation:
Technological Advance.
It's big.
Large system testing. (Lot's of TAL_Rs)
State based combinational system.
Memory System.
Beer.
Drugs.
Vat Production.