ETHZ/Biology/Lab

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Main Page Biology Pespective Engineering Perspective Meet the Team Team Notes Pictures!
.:: EducatETH E. coli - In the lab ::.

In this page, you can find information on laboratory conducted to construct EducatETH E.coli. The system parts are presented again, their assembly into plasmids and the cloning plan are explained and all lab notes taken by the ETH Zurich team are accessible. If you are trying to construct EducatETH E.coli at your lab, the section Problems we faced might be useful to you. If you want to see the whole biological design of the system, please visit the Biology Pespective. Finally, photos of our lab experience are accessible under Pictures!

Todo: decide what happens with lab book (here)

Cloning plan

Parts assignment into plasmids

Three plasmids are used for the EducatETH E.coli system parts as follows:

**Plasmids and contents**
plasmid	resistance	copy type	contents	comments
pbr322	ampicillin	high	1,2,3	constitutive subsystem
pck01	chloramphenicol	low	4,5,8,9	reporting subsystem
pacyc177	kanamycin	low	6,7,10,11	learning subsystem, reporting subsystem

It is important to insert parts responsible for the production of fluorescent proteins in low copy plasmids, as they are potentially harmful for the cell. Unfortunately, working with low copy plasmids makes the procedure more demanding in the lab.

Linkers

Because the plasmids used were not standard plasmids found in the registry, but came from the lab where we work, linkers compatible with the standard BioBrick assembly have to be used in order to work with them. The list of all linkers is the following:

**Linkers for plasmids**
Linker	Plasmid
pbr322-1	pbr322
pbr322-2	pbr322
pbr322-3	pbr322
pbr322-4	pbr322
pck01	pck01
pck01-2	pck01
pacyc177-1	pacyc177
pacyc177-2	pacyc177

Note that four linkers are tested for pbr322, as two are used for the tetracycline-resistance version of pbr322 and two are used for the ampicillin-resistnace version.

Procedure

The standard BioBrick assembly will be used to put the parts in the plasmids. Detailed information on how the BioBrick part fabrication works can be found [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication here]. For a shorter explanation of how to assemble 2 parts together check [http://partsregistry.org/Assembly:Standard_assembly here].

DNA assembly process ([1]) (Fig. 4)

Note that the composite part is constructed from the end to the beginning, i.e. each new part is inserted before the existing one. In the following, the plasmid containing the new part to be inserted will be referred to as the donor and the plasmid accepting the new part will be referred to as the acceptor. Composite pars made of parts a and b are denoted a.b.

Plasmid 1 (pbr322ap)

Put parts 1,2,3 in pbr322ap plasmids.
Merge plasmid containing part 2 (donor) with plasmid containing part 3 (acceptor). You should get a plasmid containing a 2.3 composite part.
Merge plasmid containing part 1 (donor) with plasmid containing composite part 2.3 (acceptor). You should get a plasmid containing a 1.2.3 composite part.

Plasmid 2 (pck01cm)

Put parts 4,5,8,9 in pck01cm plasmids.
Merge plasmid containing part 4 (donor) with plasmid containing part 5 (acceptor). You should get a plasmid containing a 4.5 composite part.
Merge plasmid containing part 8 (donor) with plasmid containing part 9 (acceptor). You should get a plasmid containing a 8.9 composite part. Note: this step can be done simultaneously with the above.
Merge plasmid containing composite part 4.5 (donor) with plasmid containing composite part 8.9 (acceptor). You should get a plasmid containing a 4.5.8.9 composite part.

Plasmid 3 (pacyc177km)

Put parts 6,7,10,11 in pacyc177km plasmids.
Merge plasmid containing part 6 (donor) with plasmid containing part 7 (acceptor). You should get a plasmid containing a 6.7 composite part.
Merge plasmid containing part 10 (donor) with plasmid containing part 11 (acceptor). You should get a plasmid containing a 10.11 composite part. Note: this step can be done simultaneously with the above.
Merge plasmid containing composite part 6.7 (donor) with plasmid containing composite part 10.11 (acceptor). You should get a plasmid containing a 6.7.10.11 composite part.

Problems we faced

Lab book

Week 1

Date	Completed	People
Mon, 06. Aug. 2007	Preparing the Solutions	Sylke Raphael Stefan Markus Martin Christos Joe
Tue, 07. Aug. 2007	Prepare competent cells for all parts Transformation of all the parts	Sylke Raphael Stefan Markus Martin Christos Joe
Wed, 08. Aug. 2007	Preparing the grown cultures (12) for the MINIPREP (o/n cultures)	Raphael Stefan
Thu, 09. Aug. 2007	MINIPREP of the grown (10) o/n cultures Gelelectrophoresis of the grown cultures (step: 0.8% Agarose)	Raphael Stefan Martin Christos Joe
Fri, 10. Aug. 2007	7 working parts/plasmids (step after "DIGESTS"): (B0034, R0062, R0053, E0434, B0015, R0010, E0422) 4 parts/plasmids minipreped: (R0040, R0051, Q04121, C0053)	Christos Markus Stefan
Sat, 11. Aug. 2007	no labwork
Sun, 12. Aug. 2007	labwork cancelled

Week 2

Date	TODO's	Completed	People
Mon, 13. Aug. 2007 start at 3 pm	Prepare competent cells Transformations of J23100, J37033, Q04400, Q04510 Control Restrictions (step after "MINIPREP") R0040, R0051, Q04121, C0053	o/n culture (E.Coli Top10) Control Restrictions (didn't work)	Martin Markus Christos Tim
Tue, 14. Aug. 2007	Morning Shift: Start Preparing competent cells (for J23100, J37033, Q04400, Q04510) Evening Shift: Transformations of J23100, J37033, Q04400, Q04510	Morning Shift: Prepared competent cells (stored in the -80°C freezer in the basement) Evening Shift: Transformation of J23100, J37033, Q04400, Q04510 and R0040, R0051, Q04121, C0053 (in the 37°C incubator until Wednesday) Prepared new Liquid LB, LB Agar (both in the autoclave), Agarose Gel with concentrations of 0.8% and 2.4%	Morning Shift (9am-1pm?): Markus Tim Evening Shift (5pm-...): Martin Christos
Wed, 15. Aug. 2007	Ligation (step: "LINK ASSEMBLY"): R0053 + E0422 R0010 + E0422 R0010 + E0434 S/P: R0053, R0010 X/P: E0422, E0434	Ligation didn't work due to bad quality of enzymes (probably)	From 12: Martin Markus
Thu, 16. Aug. 2007	Miniprep (J23100, J37033, Q04400, Q04510, R0040, R0051, Q04121, C0053) Transformation of #13 and #14	Miniprep of #4 (J23100), #5 (J37033), #8 (Q04400), #11 (R0040), #12 (R0051), #15 (Q04510) One batch is miniprepped (after step 19 in the miniprep procedure) and a second batch is frozen as a backup (which is to be miniprepped from step 3 on) Transformation of #13 (Q04121) and #14 (C0053) Numbers #13 and #14 are now growing in the 37°C incubator (step 13 in the transformation procedure)	Markus Christos (Martin)
Fri, 17. Aug. 2007	o/n of #13 and #14 Check whether miniprep of parts #4 #5 #8 #11 #12 (#13 #14) #15 was successful	#13 and #14 didn't grow # 4, 8 and 11 had the plasmid, they were streaked out new on plates, that we have them now on plates New white pipette tips prepared (autoclave) New bottles of Liquid LB and LB Agar prepared (autoclave)	Martin
Sat, 18. Aug. 2007
Sun, 19. Aug. 2007

Week 3

Little rearrangements of the parts. Planning of the sequences to order them.

Week 4

Date	TODO's	Completed	People
Mon, 27. Aug. 2007
Tue, 28. Aug. 2007
Wed, 29. Aug. 2007
Thu, 30. Aug. 2007
Fri, 31. Aug. 2007
Sat, 01. Sept. 2007	Transform pbr322, pcyc177 and pck01	Transform pbr322, pcyc177 and pck01 and plated them	Stefan
Sun, 02. Sept. 2007	Prepare o/n of pbr322, pcyc177, pck01	o/n of pcyc177, pck01 the plates of pcyc177 and pck01 are in the fridge transformed pbr322 because the culture didn't grow on the plate	Stefan

Week 5

Date	TODO's	Completed	People
Mon, 03. Sept. 2007	Prepare new competent cells Miniprep pcyc177 and pcK01 prepare new o/n culture of pbr322 Run agarose gel of Minipreped plasmids	New competent cells prepared, they are now in the -80° Frezzer in the basement, column #17, dark orange box (we have now 30-35 EDTs of competent cells...) Minipreped pcyc177 and pck01 (in the -18° freezer, where the antibiotics are) pbr322 didn't grow again, so no o/n could be prepared, but we get a culture from Andy on tuesday new o/n of pcyc177 and pck01 prepared (3 Falcons each), because we need to have more plasmids 2 boxes of blue pipette tips are in the autoclave Stefan ran the agarose gel (?)	Martin Stefan
Tue, 04. Sept. 2007	Miniprep pcyc177 and pck01 cut the prepped plasmids to test if we've got the right ones run agarose gel to test the cut and uncut ones prepare new o/n of pbr322 (from Andy)	Miniprep of pcyc177 and pck01 (but not yet tested) Prepared 3 o/ns of pbr322 (finally ;-) and each 1 o/n of pcyc177 and pck01, just in case there are problems with the miniprep	Martin Christian
Wed, 05. Sept. 2007	Miniprep of pbr322 Test-Digest of pcyc177 and pck01 and agarose gel... Streak out all three plasmids on new plates, so we have them in reserve	New Plate of pbr322. Minipreps and Agarose Gels will be done tomorrow	Martin
Thu, 06. Sept. 2007	Miniprep of pbr322, pacyc177, pck01 Test with agarose gel	Gel of the older plasmids -> plasmid present	Christian
Fri, 07. Sept. 2007	Miniprep of pbr322, pacyc177, pck01	Plasmids miniprepped	Martin
Sat, 08. Sept. 2007
Sun, 09. Sept. 2007

Week 6

Date	TODO's	Completed	People
Mon, 10. Sept. 2007	Miniprep pBR322 annealing of different MCSs Digest of pCK01 with BamHI+AseI digest of pACYC177 with BamHI+PstI digest of pBR322 with EcoRI+PstI all digests o/n	Christian
Tue, 11. Sept. 2007	Gelextraction of backbones pBR322, pCK01, pACYC digest did NOT work 1x ligation of MCS inside backbones o/d, Trafo 1x ligation of MCS inside backbones o/n	plate all 3 plasmids for new minipreps	Christian
Wed, 12. Sept. 2007	Trafo of o/n ligations o/n cultures of putative clones		Christian
Thu, 13. Sept. 2007	Minipreps of putative clones pCK01-MCS and pBR322-MCS control digests of putative clones new o/n cultures of the putative clones of o/n ligations		Christian
Fri, 14. Sept. 2007	separation of control digests of putative clones	*pBR322-MCS (Tet-selection) clone2 positive	Christian
Sat, 15. Sept. 2007
Sun, 16. Sept. 2007

Week 7

Date	TODO's	Completed	People
Mon, 17. Sept. 2007	new digest of pACYC177 with BamHI+PstI o/n digest of pACYC177, pBR322 AP ligation of 177 and 322AP	digest of pBR322 AP (the concentration of DNA was too low for pacyc177...) ligation of pBR322 o/n 100 ml o/n culture to MAXIprep pacyc177 Transformation of pBR322 AP to have it on plates (because andy only miniprepped them)	Christian Martin, Raphael
Tue, 18. Sept. 2007	different control digests of pBR322-MCS (Tet) (see last week) separation of pACYC177 digest Test Digests of pck01 with XbaI, SpeI, PstI, Xba/Pst, Xba/Spe (because all of them should be in the plasmid due to the sequence, and if they are it would be crap!!!) Transformation of the ligated pbr322 AP (MCS) Prep pacyc177 Digest prepped pacyc177	> no DNA on pACYC177 digest-gel, only degradation smear Plates of pbr322 AP grew No Digest of pck01 worked due to too low DNA concentration... (che cazzo di low copy plasmids !!!!) Miniprepped only 20 ml of the pacyc o/n culture with Quiagen Kit, the results were great! We have loads of DNA! (thank god! ) Digest of pacyc177 with BamHI (45 µl), then precipitated, in the gel was still very much DNA, but there were still 3 bands, so we guess, that it hasn't cut, maybe because the BamHI in the center is very old, perhaps we should Digest it in Höngg again. Digest of pacyc177 with PstI o/n (pray that it will work!) New o/n cultures of pck01 (to prep it like pacyc177), pbr322 AP (to prep it too, to have something on stock again, if the ligation didn't work), top10 (to make new competent cells) test digest of pck01 with notI, but due to the low DNA concentration I don't think it will work. I took glooves, if it now work, then we have caught some DNases in the earlier test digests	Christian Martin Raphael
Wed, 19. Sept. 2007	o/n culture of pbr322 AP (MCS), then test digest and see if it is ligated Prep of pck01 and test digests (xba, pst, spe, pvuI, notI) check the digests of pacyc177 (pst) and pck01 (notI) design new linkers for pck01, design primers for PCR for the extraction of SpeI from pck01
Thu, 20. Sept. 2007
Fri, 21. Sept. 2007
Sat, 22. Sept. 2007
Sun, 23. Sept. 2007

Week 8

Date	TODO's	Completed	People
Mon, 24. Sept. 2007
Tue, 25. Sept. 2007
Wed, 26. Sept. 2007
Thu, 27. Sept. 2007
Fri, 28. Sept. 2007
Sat, 29. Sept. 2007
Sun, 30. Sept. 2007

Week 9

Date	TODO's	Completed	People
Mon, 1. Oct. 2007
Tue, 2. Oct. 2007
Wed, 3. Oct. 2007
Thu, 4. Oct. 2007
Fri, 5. Oct. 2007
Sat, 6. Oct. 2007
Sun, 7. Oct. 2007

Week 10

Date	TODO's	Completed	People
Mon, 8. Oct. 2007
Tue, 9. Oct. 2007
Wed, 10. Oct. 2007
Thu, 11. Oct. 2007
Fri, 12. Oct. 2007
Sat, 13. Oct. 2007
Sun, 14. Oct. 2007

References

[1] [http://partsregistry.org/Assembly:Standard_assembly Standard Assembly Process]

@@ Line 9: / Line 9: @@
 Todo: decide what happens with lab book ([https://2007.igem.org/ETHZ/Lab_book here])
-=='''.:: Cloning plan::.'''==
+==Cloning plan==
-==='''.:: Parts assignment into plasmids::.'''===
+===Parts assignment into plasmids===
 Three plasmids are used for the EducatETH <i>E.coli</i> system parts as follows:
@@ Line 33: / Line 33: @@
 It is important to insert parts responsible for the production of fluorescent proteins in low copy plasmids, as they are potentially harmful for the cell. Unfortunately, working with low copy plasmids makes the procedure more demanding in the lab.
-==='''.:: Linkers::.'''===
+===Linkers===
 Because the plasmids used were not standard plasmids found in the registry, but came from the lab where we work, linkers compatible with the standard BioBrick assembly have to be used in order to work with them. The list of all linkers is the following:
@@ Line 65: / Line 65: @@
 Note that four linkers are tested for pbr322, as two are used for the tetracycline-resistance version of pbr322 and two are used for the ampicillin-resistnace version.
-==='''.:: Procedure::.'''===
+=== Procedure ===
 The standard BioBrick assembly will be used to put the parts in the plasmids. Detailed information on how the BioBrick part fabrication works can be found  [http://openwetware.org/wiki/Synthetic_Biology:BioBricks/Part_fabrication here]. For a shorter explanation of how to assemble 2 parts together check [http://partsregistry.org/Assembly:Standard_assembly here]. [[Image:Assembly _process.png|thumb|300px|DNA assembly process ([1]) '''(Fig. 4)''']] Note that the composite part is constructed from the end to the beginning, i.e. each new part is inserted ''before'' the existing one. In the following, the plasmid containing the new part to be inserted will be referred to as the ''donor'' and the plasmid accepting the new part will be referred to as the ''acceptor''. Composite pars made of parts '''a''' and '''b''' are denoted '''a.b'''.
-===== '''.::Plasmid 1 ''(pbr322ap)''::.''' =====
+==== Plasmid 1 ''(pbr322ap)'' ====
 # Put parts 1,2,3 in  pbr322ap plasmids.
@@ Line 75: / Line 75: @@
 # Merge plasmid containing part '''1''' ''(donor)'' with plasmid containing composite part '''2.3'''  ''(acceptor)''. You should get a plasmid containing a '''1.2.3''' composite part.
-===== '''.::Plasmid 2 ''(pck01cm)''::.''' =====
+==== Plasmid 2 ''(pck01cm)''====
 # Put parts 4,5,8,9 in  pck01cm plasmids.
@@ Line 82: / Line 82: @@
 # Merge plasmid containing composite part '''4.5''' ''(donor)'' with plasmid containing composite part '''8.9''' ''(acceptor)''. You should get a plasmid containing a '''4.5.8.9''' composite part.
-===== '''.::Plasmid 3 ''(pacyc177km)''::.''' =====
+====Plasmid 3 ''(pacyc177km)''====
 # Put parts 6,7,10,11 in  pacyc177km plasmids.
@@ Line 89: / Line 89: @@
 # Merge plasmid containing composite part '''6.7''' ''(donor)'' with plasmid containing composite part '''10.11''' ''(acceptor)''. You should get a plasmid containing a '''6.7.10.11''' composite part.
-=='''.:: Problems we faced ::.'''==
+== Problems we faced==
-=='''.:: Lab book ::.'''==
+== Lab book ==
-===='''.:: Week 1 ::.'''====
+==== Week 1 ====
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@@ Line 146: / Line 146: @@
   |}
-===='''.:: Week 2 ::.'''====
+==== Week 2 ====
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@@ Line 215: / Line 215: @@
 |}
-===='''.:: Week 3 ::.'''====
+==== Week 3 ====
 Little rearrangements of the parts. Planning of the sequences to order them.
-===='''.:: Week 4 ::.'''====
+==== Week 4 ====
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   |}
-===='''.:: Week 5 ::.'''====
+==== Week 5 ====
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-===='''.:: Week 6 ::.'''====
+==== Week 6 ====
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   |}
-===='''.:: Week 7 ::.'''====
+==== Week 7 ====
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-===='''.:: Week 8 ::.'''====
+==== Week 8 ====
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-===='''.:: Week 9 ::.'''====
+====Week 9 ====
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-===='''.:: Week 10 ::.'''====
+==== Week 10 ====
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