ETH Zurich 2006

From 2006.igem.org

standing (L-R): Marco, Alexandra, Arthur, Olga, Dimo, Marko, Robert; in front (L-R):

Franz, Michael

Adding numbers is easy, isn't it? 1234 plus 5678, for example, is 6912. But how do engineers add binary numbers instead of decimal ones? And how, in the end, can this be done by a living cell? We, the members of the ETH Zurich 2006 iGEM team, are currently working on these questions, whereas the last one seems to be not trivial.

What the addition of numbers has to do with pattern recognition, how our model and the mathematical analysis look like, and how the experiments are realized will be explained on these wiki pages. We wish you a pleasant time with our pages. Enjoy it!

Contents 1 Coordination 1.1 TODOs 1.1.1 Modeling 1.1.2 Lab 1.1.3 Documentation 1.1.4 Presentation and PR 1.2 Schedule 1.3 Participants and availability 2 finding a project 2.1 Initial project ideas 2.2 proposed projects 3 design process 3.1 system level 3.1.1 system behavorial specification 3.1.2 system structure 3.1.3 system deployment 3.1.4 system assembly procedure 3.1.5 system test procedure 3.1.6 system test results 3.2 device level 3.2.1 chemical sensing device 3.2.1.1 implementation alternatives 3.2.1.2 assembly procedure 3.2.1.3 test procedure 3.2.1.4 test results 3.2.2 light sensing device 3.2.2.1 implementation alternatives 3.2.2.2 assembly procedure 3.2.2.3 assembly progress 3.2.2.4 test procedure 3.2.2.5 test results 3.2.3 logic (half adder) device 3.2.4 reporters 3.2.5 XOR gate 3.2.5.1 implementation alternatives 3.2.5.2 modeling 3.2.5.3 assembly procedure 3.2.5.4 test procedure 3.2.5.5 test results 3.2.6 AND gate 3.2.6.1 implementation alternatives 3.2.6.2 modeling 3.2.6.3 assembly procedure 3.2.6.4 test procedure 3.2.6.5 test results 3.2.7 PoPs duplexer device 3.2.7.1 implementation alternatives 3.2.7.2 modeling 3.2.7.3 assembly procedure 3.2.7.4 test procedure 3.2.7.5 test results 3.3 parts level 3.4 modeling 3.4.1 Matlab scripts for ODE simulation 3.4.1.1 modular scripts 3.4.1.2 old scripts 4 Useful Documents & Links

Coordination

TODOs

Modeling

• Parts Model the whole System with Sensing, Pops duplexer and Half adder (Marco and Franz)
• Model whether a different strength of input is necessary for the AND and XOR Gates (Who?)
• Finish modeling the second AND Gate and find a biological way to implement it and write the DNA and order it (Marco and Robert)

Lab

Responsible: Robert for the preparatory experiments, Olga for the assembly and testing of the gates.

• Read the literature on the XOR and AND Gates, check carefully for strains needed and compatibility of the parts (Who?)
• Prepare a protocol for parts assembly (Olga)
• Assembly of the light sensing device from the parts we received from UCSF Voigt's lab (Arthur)
• Assembly of the chemical sensing device (Franz, Dimo, Robert, Marco, Marko, Olga)

Documentation

Responsible: Alexandra for the registry, Arthur for the Wiki.

• enter lab experience report to registry
• Make a picture of the whole model with te different parts in it (Alexandra) (redundant to 1 Page Overview (pdf)? --Ajk)
• Make a drawing of the DNA to have an overview of which parts will be consecutively on the same DNA piece (Alexandra) (this is part of the #system deployment section --Ajk)
• Find promoters for the Pops duplexer (2 promoters in total) (Michael)
• make poster for jamboree (who?)

Presentation and PR

Responsible: Franz for the presentation, Dimo for PR

• choose two or maximum three speakers who will present our work at the jamboree
• design and write the final presentation (with LaTex beamer class?)
• draw a team logo and find a team name
• design and order T-Shirts

Schedule

Available as Google Calendar: iGEM 2006 ETH Zurich

Thu 20.7., 1700: kickoff meeting in CNB E 121

27.7.-3.8. 1st group phase

Define project in more detail within two groups
Thu 27.7., 1700: meeting of entire group to share ideas
Thu 3.8., 1700: decision on final project

15.8. 1700

Tutorial "Modelling of AND gate"

Until 20.8.

Finalize DNA design, order it

September,October

Implement design (registry bio-bricks, ordered DNA)

27.9.

Fix the flight dates and send the proposed flights to Jörg

23.10.

Latest point to start getting our presentation going and to finish the iGEM wiki documentation

30.10.

Project documentation on the Wiki has to be complete

4./5.11.

Jamboree in Boston

Participants and availability

• Michael Friedmann:
• Dimo Brockhoff:
• Franz Zürcher:
• Olga Nikolayeva:
• Alexandra Choutko:
• Arthur Korn:
• Robert Schütz:
• Marco Terzer:
• Marko Jovanovic:

finding a project

Initial project ideas

The fruits of some brainstorming and research

proposed projects

We split up the whole team into two groups, each proposed a project after these two weeks.

• Meat monitor project (Michael, Dimo, Olga, Arthur, Marko)
• Half adder/pattern recognition project (Franz, Alexandra, Robert, Marco)

It was decided to further pursue the Half adder project idea.

design process

This could be documented as a hierarchy of global specification -> structural specification steps (ie after-the-book engineering process). Even if nobody had that in mind probably we can mold wathever actually happened into this pattern.

system level

system behavorial specification

1. Write something with a chemical on a petri plate (like ETH for example)
2. Let Bacteria grow uniformly on the plate
3. Expose the plate to a picture (black and white) of the same pattern
4. Result:
   • Bacteria gets green when pattern on the plate and picture match (light and chemical)
   • Bacteria does not express fluorescent protein when pattern on the plate and picture match (no light and no chemical)
   • Bacteria gets red when pattern on the plate and picture do not match

           light   no light
chemical     A         B
no chemical  B         C

The outputs can be reported by fluorescent proteins, the mapping of states to outputs is arbitary, our choice is:

A: green
B: red
C: no fluorescence

Considering the green and the red output as being separate, the logic mapping the input states to the output states is AND for the GFP and XOR for the RFP. Together they amount to a half adder logic.

The whole system is only considered at it's steady state, dynamic processes are only of minor interest.

system structure

The whole process can be brought into a common input, logic, output form:

[light sensing]----->[       ]-->[reporter A]
                     [ logic ]
[chemical sensing]-->[       ]-->[reporter B]

system deployment

distribution on the plasmids, strains

system assembly procedure

system test procedure

system test results

device level

chemical sensing device

The chemical sensing device's PoPs output activity should be a monotonic function of the concentration of a certain substance in the cell's environment.

implementation alternatives

1. Lactate lacI represses, IPTG induces (BBa_R0011 or BBa_R0010 )
2. Tetracycline, TetR inhibitor, Tet inducer by inhibiting TetR (or aTc, it's analog) (BBa_R0040)
3. combination thereof (BBa_I13614 / BBa_13617 / BBa_I13623 / BBa_I13624 / BBa_I13627 / BBa_I13637 / BBa_I13653)
4. simple sugar Arabinose (BBa_R0080)

I see the main difficulty in the spatial separation as the cells are growing in the petri dishes. since the inducers are water-soluble we would have to fix the chemicals onto the petri dish.

assembly procedure

where we got it and link to theyer documentation

Progress:

2006/10/03

Made LB-Agar plates with antibiotics

2006/10/04

Transformed cells, plated them

2006/10/05

Found plates empty after 18h on the table, put into incubator at 37°C

2006/10/06

picked cultures onto fresh plates

test procedure

test results

light sensing device

The light sensing device's PoPs output activity should be a monotonic function of the light intensity the cell is subjected to.

implementation alternatives

show how the existing light sensing device fullfills our specifications

assembly procedure

Olga got the strain RU1012(KmR) and the plasmids pCPH8(CmR) and pPL-PCB(AmpR) from Christopher Voigt <cavoigt at picasso.ucsf.edu&gt [Engineering Escherichia Coli to see light; Nature vol. 438.].

A autonomous light sensing system can be obtained by cloning those two plasmids into the strain.

1. plate RU1012 on LB+Km
2. pick RU1012 cultures -> 5ml liquid culture (LB+Km)
3. 1. inoculate 200ml liquid culture
   2. grow for 3h
   3. wash twice (that means centrifuge, pipet off the liquid, dissolve in fresh LB?)
   4. make them competent
   5. make samples
   6. transform with both pCPH8 and pPL-PCB
   7. plate on
      1. LB+Cm
      2. LB+Ap
      3. LB+Ap+Cm
4. 1. if cultures survive on the Ap+Cm plate inoculate liquid culture 5ml LB+Km
   2. run tests

assembly progress

2006-10-16

1. poured LB+Km plates --Ajk
2. inoculated RU1012 on a LB+Km plate --Ajk

2006-10-17

1. picked a RU1012 colony and inoculated a 5ml liquid culture (LB+Km) --Ajk

2006-10-18

1. diluted the RU1012 liquid culture to 200ml and incubated it again --Ajk

test procedure

test results

logic (half adder) device

Registry: BBa_J34000

As stated in the #system behavorial specification the logic is made up of one AND and one XOR gate, which are each another device, plus two copy devices to replicate the inputs:

       [          ]------>[     ]
A >----[ 1:2 copy ]       [ AND ]----> X
       [          ]--, ,->[     ]
                      X
       [          ]--' '->[     ]
B >----[ 1:2 copy ]       [ XOR ]----> Y
       [          ]------>[     ]

reporters

XOR gate

The XOR gate's PoPs output activity should be correlated to the PoPs input activity as shown in the picture:

 input A ^
         | H  D  L
         | D  D  D
         | L  D  H
         +--------->
            input B

 output: High, Low, Dont care

implementation alternatives

Part to be used in the prototype system: BBa_J34200

modeling

assembly procedure

test procedure

test results

AND gate

The AND gate's PoPs output activity should be correlated to the PoPs input activity as shown in the picture:

 input A ^
         | L  D  H
         | D  D  D
         | L  D  L
         +--------->
            input B

 output: High, Low, Dont care

implementation alternatives

Part to be used in the prototype system: BBa_J34100

modeling

assembly procedure

test procedure

test results

PoPs duplexer device

This device has two PoPs outputs which should in terms of activity be copies of the input.

implementation alternatives

modeling

assembly procedure

test procedure

test results

parts level

for every part we use:

• DNA sequence
• where we got it from

(links to the registry)

Maybe this could mostly be a hierarchy of links to the registry because it's preferable to have as much documentation in the registry as possible anyway. This is nice because it emphases our incredibly systematic engineering approach and documents the processes too which could also serve for coordination of the work in progress.

modeling

The contents of this section should be placed at the appropriate places in the design process section above and the rest moved to an external page.

Matlab scripts for ODE simulation

modular scripts

• contains a createXXX() script for each module. the created module contains
  • function handles for reaction rates: r
  • stoichiometric matrix: N
  • constants (inside of the function handles)
  • state (concentration) changes (the ode dy values) can be computed by: N · r
• modules can be connected using the createInOutConnector() script. the result is again a module, consisting of the connected basic modules.
• sim_1_1 and sim_1_2 can be used to simulate modules with 1 input/1 output and 1 input/2 outputs respectively.
• both basic modules and compound (connected) modules can be simulated
• simulations contains the first samples, simulating
  • XOR → simulation results / sensitivity analysis
  • AND-tRNA → simulation results / sensitivity analysis
  • IPTG Sensing →simulation results
  • PoPS Duplexer →simulation results
  • Compound module: IPTG Sensing → PoPS Duplexer →simulation results
• scripts: matlab_modules.zip (<0.1M)

old scripts

unzip the file, each zip file contains 2 files: sim_xxx.m and ode_xxx.m.

ode_xxx.m : contains the differential equations, i.e. the model

sim_xxx.m : sets the parameters, calls the simulator and plots the result (this is the one to run, but the other is also needed).

• matlab_sim_and1.zip (<0.1M) →simulation results → abandoned
• matlab_sim_and2.zip (<0.1M) →simulation results → the pursued version A
• matlab_sim_and3.zip (<0.1M) →simulation results → the pursued version B
• matlab_sim_and4.zip (<0.1M) →simulation results → abandoned

As a result of the meeting on August 17, we will from now on concentrate on the AND versions 2 and 3.

• matlab_sim_xor1.zip (<0.1M) →simulation results → the only pursued version
• matlab_sim_xor2.zip (<0.1M) →simulation results → abandoned
• matlab_sim_xor3.zip (<0.1M) →simulation results → abandoned

Sensoring

• matlab_sim_iptg.zip (<0.2M) →simulation results

Useful Documents & Links

see here