Page History

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.

======================================================================================================

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.

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

-

Implementation:

Cas9,

Guide

RNA

for

repression.

mRNA

sensing

repression.

======================================================================================================

Updated

Powerpoint

with

improved

sprites

and

arrow

pushing.

V2

======================================================================================================

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.

======================================================================================================

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

======================================================================================================