Alberta/Calender/August
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August 1
Schedule: CZ,NG,VH
General Notes:
1. Run gel of B0034 SpeI/PstI double digest; extract gel with QIAgen kit; stored in freezer.
2. PCR for
a. Enny + B0034 miniprep 1 to 8
b. Betty colonies (10)
c. Buddy colonies (10)
Follow James' protocol. Also see blackboard for James' comment about PCR.
For tomorrow
1. run gel of PCR prodcut which are in the thermocycler �
2. check restreaked single colonies of the Betty and Buddy colony PCR
3. grow up Betty and Buddy overnight and for miniprep and ligation later
4. Make Amp plates (we only have 4 more)
5. Autoclave test tubes
Quotes of the day: We are tired.
August 2
Modeling Meeting @ 1830hrs in CAB373
General Meeting @ 1900hrs in CAB373
Party afterward's @ Garneau pub
Schedule:
MC, JP & AF are meeting at 1700hrs to get some stuff done before the meeting happens; come join in the fun if you'd like.
Lab Notes:
Made AMP plates
Autoclaved test tubes
Ran gel of ?
Started O/N of Buddy & Betty
Checked restreaked colonies of Buddy & Betty --> positive growth except for 9&10 but this is expected because they are controls
James did a loving PCR of Benny in B0034
-MC, ED, JP, JB
August 3
Schedule:
Nik cant make it he just isn't crazy enough looks like justin is currently the only one crazy enough
Michelle & Justin are now the long weekend crew - be prepared for ILLUSIONS!!!! or perhaps just some awesome pipetting techniques while they're prepping to champ out at the ULTIMATE pipetting Olympiads.
Meeting @ 1700hrs
Captain's Log, Stardate: 080307-1153
Minipreps of lifeforms Buddy and Betty
Not enough room in box with blue tape, designed a new holding vessel (i.e. box with white tape below box with blue tape in the freezer) for minipreps of aforementioned lifeforms.
-JB
Made gel
Digested (double) Buddy & Betty minipreps
Digest (single) I0500 - from tube we believe is a miniprep in the -20 freezer
weekend to-do list
-JP, ML, MC
August 4
Meeting at 1000hrs - Michelle will definately be there at 1000 Justin is expected at 1030
Lab Notes:
Made a project timeline - check out the cabinets on the left side of the 4C-degree fridge
Ran gel - no bands for I0500 (we were sad) but there are awesome bands of Betty & Buddy
Attempting to figure out the I0500 problem; transformed into XL10 Gold & HB101
-MC, JP, ML
August 5
Meeting at 1000hrs - Michelle will definately be there at 1000 Justin is expected at 1030
Lab Notes:
1-transform I0500 into HB101 and XL10 gold
2-restricted mini's of Buddy and Betty with Xba/Pst (confirmed with gel their presence yesterday)
3-ran I0500 samples in gel and no DNA present, chucked out samples - re transform...
-MC, JP & ML (in spirit)
For Tomorrow
1-gel purify Buddy and Betty
2-ligate Buddy and Betty into Boo34 (overnite)
3-start ONs of I0500 for mini on tuesday
August 6
Meeting at 1000hrs - Michelle will definately be there at 1000 Justin is expected at 1030
Lab Notes:
- JP, ML, AF, MC
Notes:
1- re-plated I0500 tranformations on Kan and AMP plates - hope for growth
2- ran buddy and betty XbaI/PstI restriction products on gel and gel extracted
3- began ligation reaction with B0034 (in back shaker at 13 degrees)
4- started making butanol plates...but it might not work so well with higher percentages because when you plate the agar its warm/hot and when you add the butanol it bubbles like mad (evaporates). We tried pouring at lower temp, but it prooved disasterous
Fact of the Day
A good ligation is like a hoola-hoop, they're both circular and only one is methylated
August 7
Schedule:
MC,VH,AF
Protocol for Today
1: If there is growth on I0500 plates in 37degrees, make some overnites of 5 colonies (4ml LB + 2.4microL KAN [in buffer box]in shaker tubes and innoculate with bacterial colony and place in shaker at 37degrees overnite -circle each colony you pick and match with respectively labeled shaker tube)
2: Take the two ligation mixtures from the back room shaker- transform into XL10Gold bacteria- for each of the sample make two dilutions.
dilute (1)2microL into 8microL water and
(2)1microL into 9microL water.
Take the four samples and transform them (dilute in 600microL LB before puting into shaker.
Plate each transformant onto AMP plates in two dilutions:
(1)200microL on a plate
(2)50microL + 50microL LB.
Lab Notes:
No growth on Kan plates of I0500 in HB101 - therefore no O/N
Transformations of Buddy+B0034 Ligations & Betty+B0034 Ligations into XL10GOLD competent cells
- Betty+BOO34 10x = 1ul Lig + 9ul H20 (the number on the side of the eppendorf denotes the ratio of vector to insert in the lab book) 20x = 2ul Lig + 8ul H20
- labelling same for Buddy+BOO34
- MC, VH, AF
August 8
Today is sweatpants day. Wear your favorite pair.
The last of the synthetic genes has arrived (butyraldehyde dehydrogenase = BuAld_DH). I resuspended the plasmid in 40uL TE and put the red capped tube (with a pink tape flag) in the freezer in G308 - MKD
LAB NOTES:
1: transformed buAld_DH "Diezel Blaze" into XL10 gold need to grow up for mini tomorrow nite
2: colony PCR on buddy and betty in Boo- reactions are in PCR machine (hopefully at 4 degreesC)
3: started Chlorobium medium/concoction need some more compounds
-JP,ED,AF
Schedule:
ED,NK,JP
August 9
Schedule:
ED,AF,JG
Lab Notes: -poured 1%-4% butanol-LB plates - added butanol to each individual plate as it was cooling. plates are on bench #3
-ran gel of PCR of Buddy and Betty in Boo. Looks like all colonies tested were positive. Started overnights of positive colonies for glycerol stock and miniprep tomorrow.
-set up PCR using VF and VR and 0.5 uL of 1/10 dilution of I0500 stock as template. Mg titration of 1,2,3 mM. Need to be run on gel tomorrow
-started overnights of Diezel Blaze for miniprep and glycerol stocks
-ED,MC,JG
Modeling meeting cancelled as Nick G. and Doug are both away - WM
August 10
Schedule:
CZ, ML, JG
Thanks for taking my shift ML - MC
Please note that if you cannot make a shift we have already discussed that you are to call the lab phone number which is in previous minutes - I can send it out with the next minutes just in case. - MC&JG
Lab Notes:
Minipreps and glycerol stocks of Buddy and Betty in Boo and Diezel Blaze were done and stored in box with green tape.
Tonight: run I0500 PCRs on gel, digest Diezel Blaze to clone into Boo, start mutagenesis experiments, transform some new promoters
This weekend: we can start cloning our genes into J61003 with this promoter and then swap the promoters later if we want (this was the reason for picking J61003), also we need to wash and autoclave culture tubes
-ED
Lab Notes
Ran gel of pcr product no bands where observed. PCR reminants are stored in -20 freezer.
Double digest of diesel blaze pst1 xba1, Stored in -20 freezer
Gel already prepared on the second bench.
Culture tubes have been wash but need to be autoclaved tommorrow
ACTION ITEM: decide on promoter to transform we promoter list is on the mac computer.
Uplifting thought:
A negative result is still a useful result. As long as it is within errors it is still valid.
August 11
Schedule: 9:00am sharp as a needle
JP, AL, NK
1. got a hold of Meagan at MIT and she's sending a stub of IO500 bacteria. we should get it early next week I hope!
Lab Notes:
1- organized all important samples into new box in -20 (all coding sequences in Boo) These will need to be restricted with Xba/PST for ligation into J61003 later
2-started ligation on Diezel into Boo (samples at the front of the room on bench - need to transform tomorrow asap)
3- autoclaved
August 12
Schedule:
CZ, AL, NK
Celine: wanna meet up at noon? AL
Lab Notes There was a misunderstanding about the Diezel Blade double digest. On Friday, we only did the digest but did not run a gel or perform gel extraction. So the ligation mixture from Saturday was discarded because B0034 was ligated to the double digest mixture directly.
Today we ran the remaining double digest mixture; however it did not cut.
Also we transformed Bba_I13453 (pBAD promoter by itself) just in case on Amp plates, which are in 37 degree incubator.
For tomorrow 1. Take out I13453 plates and put in 4 degree fridge (Celine will do this early morning around 8am) 2. Pick colonies for I13453 and grow in Amp-LB overnight 3. Double-digest of Diezel, run gel, gel extraction, ligation with B0034.
Justin, can I swap with you for Monday because I may not make it on Thursday if we are doing labwork before the meeting? Email me to confirm. Thanks. - CZ
August 13
Schedule:
ML,JG,JP
Omniscient Notes:
1- Label Tubes Well - There is nothing worse than having to redo your samples because you don't know what each tube is. Aside of our coding namings Benny, betty etc, Label in detail. Always put the date on the tubes so we can always refer to the master book if we're confused
MC available in AM to do some lab work - if needed please notify via email - MC
I took out plates for I13453 this morning and there are big colonies to pick tonight.
August 14
Schedule: MC,JP,ML
August 15
Schedule: CZ,AL,NK
August 16
Schedule:
JP,CZ,AL If lab can happen before meeting we can just leave for erins house after the meeting so you three should look into that JG
I most likely cannot meet at the lab before the meeting, but if either Erin or Justin can. I would be willing to swap. Please let me know ASAP, thanks.-CZ
Post-meeting video/board game party at Erin's house if there is interest.
August 17
Schedule:
ED, AF, JG
August 18
Schedule:
ED, AL, NK
Hey guys i cant make it on 17,18 or 19. I have to go to seattle. Can someone switch with me please. Thanks -NK
August 19
Schedule:
CZ, AL, NK
August 20
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