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September 7, 2006

Obtained purified DNA of I0500 (2005) with a concentration of 0 ng/uL. Try again tomorrow

Made mini-preps of B0015 (2005) and I13507 (2005) and made a plate of B0031 (2005)

Part NamePart DescriptionParts MatchPlasmid Match
B0015 (2005)Terminator----
B0031 (2005)Medium RBS--O
C0056 (2005)Repressor protein 434 cI--O
I13507 (2005)RBS.mRFP.Terminator----

Do it all again except B0031 (2005) because part length ~14 bp. C0056 ~ 800 bp when it should be 636 bp and I13507 had really fat bands.

To-Do List:

  • Purify I0500 (2005) at a higher concentrating (X3) (tape wells together)
  • Purify E0240 (2005) while testing part lengths of B0015 (2005), C0056 (2005) and I13507 (2005) again
  • Check compatibilities with cI plasmids and I12006 + E0240
  • Ligate Parts I0500 (2005), J06801 (2006), E0240 (2005)

Construction Home

September 6, 2006

We started the mini-prep procedure for B0015 (2005) and I13507 (2005) by preparing an o/n growth of cells. We then prepared freezer stock of J06801 (2006), B0034 (2005), C0056 (2005), E0240 (2005), I0500 (2005), I12006 (2005).

We began the ligation procedure using I0500 (2005) and J06801 (2006). We were only able to get J06801 to work so we proceeded with the quantitation of that part only. We obtained 3.0 ng/uL of purified J06801 DNA ready to be ligated tomorrow.

To-Do List:

  • Repeat ligation attempt using I0500 (2005) and maybe continue with E0240 (2005)
  • If plasmids are compatible, we can ligate I12006 (2005) and E0240 (2004) and co-transform with a plasmid that expresses cI
  • Transform B0031 (2005) to make a freezer stock after 2 days.
  • Complete MP procedure for B0015 (2005), I13507 (2005)
  • Then check part/plasmid length, (with double digest), of B0031 (2005), C0056 (2005), B0015 (2005), I13507 (2005)

Construction Home

September 5, 2006

We tested the newly prepared MPs as well as two of the parts from yesterday using a double digest (XbaI and SpeI with Buffer 2).

Part NamePart DescriptionParts MatchPlasmid Match
J06801 a (2006)Inverter with strong RBSOO
J06801 b (2006)Inverter with strong RBSOO
J06501 (2006)Repressor, LacI temp sensitiveXX
B0034 (2005)RBS (Elowitz 1999)--O
C0056 (2005)Repressor protein 434 cI--O
E0240 (2005)Medium RBS.GFP.TerminatorOO
E0422 (2005)RBS.ECFP.TerminatorXX

We transformed B0015 (2005) and I13507 (2005).

To prepare a freezer stock, we made o/n of J06801 (2006), B0034 (2005), C0056 (2005), E0240 (2005), I0500 (2005), I12006 (2005)

It now looks like we can attempt a ligation according to the first stage in the proposed CDR modules (I0500 + J06801 + E0240).

To-Do List for Tomorrow:

  • MP B0015 (2005), I13507 (2005)
  • Make a freezer stock of 06801 (2006), B0034 (2005), C0056 (2005), E0240 (2005), I0500 (2005), I12006 (2005)
  • Ligate I0500 (2005), J06801 (2006), and E0240 (2005)

Construction Home

September 4, 2006

Started the mini-prep (MP) procedure (o/n growth) on E0240 (2005), B0034 (2005), J06801 (2006) and J06501 (2005)

Obtained a MP for C0056 (2005) and E0422 (2005).

Plan to do:

  • Check lengths of E0422 (2005) and C0056 (2005)
  • Transform B0015 (2005) as a backup/practice
  • MP B0034 (2005), E0240 (2005), J06501 (2006), and J06801 (2006) -- check lengths once done
  • Make I13507 (2005/2006) -- RFP (minus a promoter)

Construction Home

September 3, 2006

We decided to recheck the more relevant parts using a double digest (XbaI and SpeI with Buffer 2). This time we compared both the plasmid length and the actual part length. Again O = match, X = no match and -- = inconclusive)

Part NamePart DescriptionParts MatchPlasmid Match
I0500a (2005)Promoter inducible by pBad/araC – part of thermometerO O
I0500b (2005)Promoter inducible by pBad/araC – part of thermometerO O
J06801 (2006)Inverter with strong RBSOO
B0031 (2005)Medium RBS--O
B0031 (2006)Medium RBSXX
C0056 (2006)DNA sequence for repressor protein 434 cIXX
B0015 (2006)Terminator--O
J04450 (2006)RFP switched off by IPTGXX
I12006 (2005)Modified lamdba Prm promoter (repressed by 434 cI)-- O
E0240 (2006)Medium RBS.GFP.TerminatorXX

Began min-prep procedure (o/n growth) for C0056 (2005) and E0422 (2005).

Transformed new parts from the 2005 DNA plate, (E0240, B0034, and J06501), and transformed more of the J06501 (2006) from the stock solution to produce more DNA for the mini-prep.

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September 2, 2006

Now that we knew the enzymes are working, we proceeded to test the MiniPreps from 2005 and 2006 (O = match, X = no match):

Part NamePart DescriptionParts+Length
Gel 1C0051 (2005)Repressor, Lambda cIX
E00433 (2005)Reporter containing LacZ alpha fragmentO
B0031 (2005)Medium RBSO
R0040 (2005)Promoter driven by tetR but action inhibited by aTcO
R0011 (2005) Promoter regulated by lacI – part of BBa_J06801 (Inverter)O
Gel 2I0500 a (2005) Promoter inducible by pBad/araC – part of thermometerO
I0500 b (2005)Promoter inducible by pBad/araC – part of thermometerO
B0031 (2006)Medium RBSX
C0056 (2006)DNA sequence for repressor protein 434 cIX
E0422 (2006)RBS.ECFP.TerminatorX
J04450 (2006)RFP switched off by IPTGX
E0240 (2006)Medium RBS.GFP.TerminatorX
R0011 (2006)Promoter regulated by lacI – part of BBa_J06801 (Inverter)X
E0433 (2006)Reporter containing LacZ alpha fragmentO

We also began the transformation of some of the 2005 parts:

  • I0500 (Promoter inducible by pBad/araC – part of thermometer)
  • C0056 (DNA sequence for repressor protein 434 cI)
  • I12006 (Modified lamda Prm promoter repressed by 434 cI)
  • E0422 (RBS.ECFP.Terminator)

Construction Home

September 1, 2006

With a lot (a LOT) of help from Seema, we now have 24 Eppendorf tubes of competent cells (DH5a-z1) in the -80C freezer. We also have ~10 plates with Ampicillin (Amp), ~8 plates with Kanamycin (Kan), and 4 plates with Amp/Kan resistance. Seema also sorted out our iGEM box and separated between the 2005 parts and the 2006 parts as well as grouped the enzymes, reagents, and ladders.

Due to a lot of problems with previous attempts at transformations and quantifications, we decided to begin testing the enzymes as well all the part lengths so that we can get a handle of what we have to work with. So we tested all the enzymes, (EcoRI, XbaI, SpeI, and PstI) using a test plasmid. In theory, the uncut plasmid should move farther in the gel than the cut plasmid because the circular plasmid is more compact and would better be able to move through the agarose gel. This was indeed the case and all the enzymes cut successfully as shown the by the 4 bands being at the same height above the uncut band.

One thing to note was that the enzyme Xba1 worked slower than the others. Since the idea was to just check if the enzymes were working, we didn’t need to let the enzymes cut for the full 1 hr (as per the protocol). Thus, we ran the gel about 40 min early and saw two bands (one for each of the cut and uncut plasmid) in the Xba1 lane.

Construction Home

August, 11, 2006

Hey team,

It looks like we'll soon be underway and get to start building and testing parts. I seem to remember Farshid saying he and Jessica already extracted the parts that we needed from the registry, so that we can move on from there. There's a semi-final outline of what we'd like to do on the Critical Design Review (CDR) page so take a look at that. Once we get approval from Prof. Davies, we can get started.

The overall idea is to "assign" a part to a member so that member is responsible for growing/maintaining that part as well as adding that part to someone else's part. Also, depending on other people's thoughts on this, it would be a good idea to double up on the parts so that we get at least two cracks at making a part at the same time. This allows everyone to participate in the process from start to finish. Of course there will be a lot of flexibility in who does what, but this gives us some sort of baseline to start with. I'll be making some sort of sign-up sheet so if you want to make a specific part for some reason you can. I was thinking of using Google calendar to help with the coordination, so if you want a Gmail address, you can just email me and I can invite you (Gmail is actually really good). I'll keep you updated on this idea though.

Finally, CHECK THE WIKI REGULARLY!! We are now going to start doing stuff so there should be regular postings on the Wiki and so I don't want to flood everyone's inboxes. I will try to see if there is some way to indicate whether a link has been modified in some way so that you know there has been an update. Or if any of you know how to implement that by all means go for it.

Charles Yoon

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