User:GeorgeXu/Notebook/iGEM 2007

Double Digest of AIDA-1 and PCRed rdm-lib
Note: NotI is only 50% efficient in Buffer 2 so I also set up a sequential digest (Nick said that one time that anything under 100% for NEB enzymes is unreliable). Also, both the PCRed rdm lib samples above and below came from the first PCR reaction (tube labeled 1 and lane one from the gel).

Sequential Digest of AIDA-1 and PCRed rdm-lib
Note: The samples were PCR purified between steps 1 and 2 for both sequential digests.

Miniprepping AIDA-1/pet29b+
Miniprepped the AIDA-1 (~150 ng/uL for all three samples; curves looked good)

PCRing Random Library
Realized we don't have NotI enzyme so set up a PCR reaction for the random library + AIDA: Both primers can be found in the -20dC freezer in the small room in a box labeled with green tape (something like "Mike Strong Plasmids for iGEM 2007"). These are primers for the 15mer library.

I used the "rdm lib pcr AIDA" (or something like that) program on the grey machine near the entrance of the big room. The program steps are:
 * 1) 95dC for 04m00s
 * 2) 35 loops of:
 * 3) 95dC for 00m15s
 * 4) 55dC for 00m30s
 * 5) 68dC for 02m15s
 * 6) 68dC for 15m00s
 * 7) 4dC forever

After the PCR, I ran a gel. The bands looked the correct size and were relatively bright.

Growing Liquid Cultures (AIDA-1/pet29b+)
Grew up 3x4.5mL of AIDA-1 in LB kan from Perry's frozen stock (loc:Perry's box in the -80dC). Tubes were labeled something like "AIDA-1/pet29b+."

Rdm lib + AIDA construction

 * 1) AP treated 50 µL of AIDA1 cut with NotI/NheI in pet29 with 6 µL AP buffer and 4 µL AP
 * 2) Clonewelled the samples
 * 3) Vacufuged and PCR purified the samples
 * 4) Nanodropped and set up three ligation reactions
 * 5) PCR digest 1 + cut AIDA
 * 6) PCR digest - 30 µL of 33.8 ng/µL lyophilized and resuspended in 13.5 µL, used 7 µL
 * 7) cut AIDA - 47 µL of 37.3 ng/µL lyophilized and resuspended in 9 µL, used 3 µL
 * 8) PCR digest 2 + cut AIDA
 * 9) PCR digest - 32 µL of 45.1 ng/µL lyophilized and resuspended in 19.4 µL, used 7 µL
 * 10) cut AIDA - 47 µL of 37.3 ng/µL lyophilized and resuspended in 9 µL, used 3 µL
 * 11) PCR digest 3 + cut AIDA
 * 12) PCR digest - 32 µL of 45.7 ng/µL lyophilized and resuspended in 19.4 µL, used 7 µL
 * 13) cut AIDA - 47 µL of 37.3 ng/µL lyophilized and resuspended in 9 µL, used 3 µL

Re-electroporating tagged Single Cells + T02 his
I had to miniprep more JT because we used up the plasmid preps from last time Plates should be in incubator
 * 1) JT DNA into AIDA his cells (from Steph's fridge liquid cultures)
 * 2) JT DNA into AIDA+strep cells (from Steph's fridge liquid cultures)
 * 3) RACE DNA into AIDA+strep cells (from Steph's fridge liquid cultures)
 * 4) RACE DNA into AIDA+strep cells (from Steph's fridge liquid cultures)
 * 5) AIDA+his DNA (from Mike's iGEM box) into T02 cells

Checking Tagged Receivers

 * Round 1
 * Colony PCRed the RAE+his, RAE+strep, and T02+strep (the T02+his plate was empty).
 * Unfortunately, there are only SybrSafe E-gels left, so no gel picture. Gel summary below (basically RAE+strep 2 and T02+strep 2-5 worked)
 * Round 2
 * Basically I redid RAE+his 1-3 and then streaked three more colonies to get RAE+his4-6. I also checked RAE+strep 2 and T02+strep 3-5 with the T7 promoter/terminator primers. Note I have two wells of RAE+strep 2 because I distrust (is that a word?) colony PCR.
 * Results were good. The RAE_strep 2 and T02 strep3-5 check out completely. It appears that RAE+his 3 also checks out. I've set up the T7 PCR reaction for that have it sitting in the black PCR machine on Stephanie's bench.

Other

 * Finally streaked those liquid cultures of the constructs we sequenced.
 * Streaked the liquid culture of pAC-luxGFP (Voigt construct)
 * miniprepped the pAC-luxGFP
 * poured several LBamp+kan plates. They should be labeled with black sharpie on the broad circular face of the plate.

Colony PCR of RACE (new)
RACE #1-3 are correct.

Gel

Fluorescent Microscopy of RACE
I picked from six samples from three plates of RACE and dipped into 10 µL of PBS:
 * RACE 37dC (new) - the new RACE transformation plate
 * Center of the colony (fluorescent)
 * Edge of the colony (nonfluorescent)
 * RACE 37dC (old) - the RACE plate the old transformation
 * fluorescent cells
 * nonfluorescent cells
 * RACE - the original RACE transformation plate
 * Center of the colony (fluorescent)
 * Edge of the colony (nonfluorescent)

Microscopy Results:
 * For the most part, the expected nonfluorescent cells are nonfluorescent and the fluorescent cells are fluorescent. However, it seems that the original plates are exhibiting stronger fluorescence than the new transformation plates which is opposite of what Nick, Harris, Bill and I observed in the transformation plates
 * I need to fix my protocol for preparing slides because I have problems with the ends of my slides drying in and some of my samples were very dilute.
 * These RACE cells didn't have the filament problems like the last RACE I grew. I'm going to retry the RACE+OHHL and RACE overnight to see if I can get some positive results.

Fluorescent Microscopy Pics

Colony PCR of JT + confirm Master Plate
JT's are whacko, the Master Plate constructs are correct. We need to re-transform JT into BL21.

Gel

Frozen Stock Part 1
Perry and I made frozen stocks of some stuff.

Mixed Cultures with same OD
I had a culture of S23I07 diluted to OD=0.057 and a culture of RAE diluted to an OD=0.059. I made a 1:1, 10:1, and 100:1 combined culture (with more of the RAE). I also had a culture of RACE that I induced with ~1 mM.

I grew these for about three hours and then checked them in the plate reader and the fluorescent microscope.

Fluorescent Microscope Results #1: Fluorescent Microscopy Pics 1
 * Not too much to say here, it seems that the cells haven't grown enough because we don't see much fluorescene yet and the OD's are still pretty low
 * One thing of note: the RACE is abnormally filamentous. Something is wrong...

I grew the samples for another two hours and then checked them again in the plate reader and the fluorescent microscope.

Fluorescent Microscope Results #2: Fluorescent Microscopy Pics 2
 * The RFP fades RIDICULOUSLY fast. The fluorescence fades to black in a couple of seconds.
 * The GFP in the mixed cultures is pretty good, the RFP is almost invisible. This could be the result of the RFP folding time and the fact that the RFP fades RIDICULOUSLY fast. Seriously, like, Nick and I basically had to say "1...2...3... GO!" to make sure we got the picture on time

8/08/07
I took plate reader data of the swab inoculated liquid cultures:

I also checked the cultures under the fluorescent microscope:
 * The S23I + RAE sample showed a lot of red colonies and a very small number of green colonies.
 * Maybe the red colonies are just much better competitors? It could also be because I didn't start with equal OD's. I'm going to redo this tomorrow.
 * The RAE works surprisingly well. By itself, it has a pretty good OFF and the induced with OHHL was brightly fluorescent.

Fluorescent Microscopy Pics

Colony PCR for Master Plate
Colony PCR is a stupid protocol

Gel

Colony PCR for Master Plate
Whaaa?

Gel

Colony PCR of luxpR Senders and Receivers
Whaaa?

Gel

Colony PCR of luxpR JT + mCherry parts
The mCherry colonies were not red T_T.

Gel

Colony PCR of mCherry Part
Most of the streaks looked good

Gel

Colony PCR of luxpR Round 2 Take 1
Colony PCR'ed the transformation plates from last night. The transformation plates looked very good, with lots of colonies.

Gel

luxpR Construction Round 2
Miniprep, Digest, Dephosphorylate, Clonewell, Ligate, Transform:
 * R0062130 ng/µL. Also, I stupidly transformed into Top10F' instead of Top10.

Colony PCR of luxpR Round 1 Take 2
I colony PCR'ed the colonies from the transformation plates from last night. The plates were a little better, with around 10 colonies each. I only got *i think* the C0061<I13504 to work. Also, the five bands that should be R0062<A340620 are all about the size of R0062 so I'm going to redo the construction tomorrow.

Gel

Colony PCR of luxpR Round 1 Take 1
Unfortunately, there were like no colonies. Meaning: So I colony PCR'ed them and then froze the result (no gel running today, folks).
 * R0062<A340620
 * Two colonies
 * C0061<I13504
 * Zero colonies
 * C0061<E0240
 * Two colonies

Religating and Transforming
I re-ligated and transformed some leftover DNA from last night:


 * R0062<A340620
 * C0061<I13504
 * C0061<E0240

Finally, I transformed the constructs into Top10 cells.

Clonewell, Vacufuge, Ligate, Transform
I clonewelled, vacufuged, and then ligated the following:
 * R0062<A340620
 * C0061<I13504
 * C0061<E0240

Finally, I transformed the constructs into BL21 cells.

Dephosphorylating the Vectors
I dephosphorylated the R0062 and C0061 with Antarctic Phosphotase and then heat inactivated them for 10m at 65dC.

Digesting for Double luxpR
I digested the following for 99:99 at 37dC:

Sequencing the C0261
I prepared and sent C0261 for sequencing.

Miniprep for Double luxpR
Perry and I miniprepped: in order to build the luxpR construct.
 * R0062
 * A340620
 * C0621
 * E0240
 * I13504

FACS
Perry and I diluted down overnight samples and grew them in an incushaker from 9:30-12:30. The numbers indicate OD right before we resuspended in PBS. We tried to resuspend so that the final OD was around 0.003.
 * JT
 * 1:10 (.555)
 * 1:100 (.141)
 * 1:1000 (.02)
 * 1:10000 (.000-.001)
 * T02&S23I07 1:1000 (.03)
 * T02&J23039 1:1000 (.03)
 * F20I07&S23E40 1:1000 (.075)
 * J04450 1:100 (.064)
 * I13522 1:100 (.62)
 * B0015 1:100 (.061)

[[Media:072707facsgx+pt.zip]]

Overnight Plate Reader Growth Curve Results
I set up a plate reader as follows. The numbers after the label indicate starting OD. Note: Our plate reader seems to have trouble reading OD's around 0.1, so I'm not completely sure if the 0.1 values are accurate. I took the lower OD readings in the OD machine in the small room, so I'm pretty confident about those.

Results:
 * Starting at OD~0.1 or OD~0.04 it took the samples around 2 1/2 hrs to read OD~0.3 and around a total of 6 hrs to hit stationary phase
 * Starting at OD~0.003, it took the samples around 4 hours to reach OD~0.3 and around a total of 7 hours to hit stationary phase
 * There didn't seem to be a big difference between starting at OD~0.1 vs OD~0.04. Of course, this could be due to the fact that I took the OD reading for the OD~0.1 samples in the plate reader, which is inaccurate in that range.
 * Overall, the samples grew at pretty much the same rate. There appears to be at most a 45-60 min lag between different constructs, but this could be due to variations in starting OD.
 * The blank LB samples were interesting. They were pretty much flat and low until around 8 hrs in, then they grew exponentially to around OD~1. This seems to indicate that there were very low levels of contamination in these LB wells. I added LB+amp to these wells, so the contamination is probably coming from our own constructs. I don't know if this contamination was present when I loaded the wells or somehow there was cross-well contamination during the reading period.

For all the graphs+raw data: [[Media:072607platereadergx.xls]]

Sorting through Sequences
I went through all the sequences we have done and compiled the results

Sequencing Results

Miniprepping, Nanodrop, and Sequencing S03608.I13507
I miniprepped and sent S03608>I13507 for sequencing. Elapsed time: 20 minutes.

Sequencing Results

Colony PCR of various parts
Perry and I colony PCR'ed the following parts:
 * F2620 >I13507
 * J37015
 * J37034
 * R0062
 * I13504
 * J37032
 * A340620
 * hisE0040mek

Gel

Liquid Cultures
Perry and I grew liquid cultures of several things:
 * T9002
 * J23039
 * S03623 >E0240
 * S03608 >E0240
 * S03623 >I13507
 * S03608 >I13507

Mike's Agar Plate Experiment
Perry and I carried out a preliminary test of Mike's Plate Reader Experiment. Protocol: We did duplicates because we took from two different overnight cultures, one that was obviously red and one that was not obviously red.
 * 1) Pipet 200 µL of overnight cultures of T9002 and spread onto LB agar plates.
 * 2) Let the plates sit at room temperature to allow the bacteria to soak in. (We let it sit for about 20 minutes)
 * 3) Pipet in 10 µL of one of each of the following into the middle of each plate.
 * 4) Overnight culture of S03623 > I13507
 * 5) Overnight culture of S03623 > I13507
 * 6) Overnight culture of S03608 > I13507
 * 7) Overnight culture of S03608 > I13507
 * 8) 2 µM OHHL

Ligating and Transforming the RP-JT and FluorSwitch
Perry and I performed the following ligations and transformations: into BL21
 * F2620 >I13507

We decided not to do the other ligations and transformations because we found out that we already have a S03623 T9002 miniprep and clonewell sucked, we were reluctant to move forward on that ligation.

Clonewell for RP-JT and FluorSwitch
I clonewelled and vacufuged all the digests I did earlier in the day. The band for J23039 >T9002 was almost invisible.

Sequencing the F2620 and E0240
I prepared a sequencing order for F2620 and E0240.

Sequencing Results

Dephosphorylate for RP-JT and FluorSwitch
I dephosphorylated the following: with Antarctic Phosphatase for 1 hr at 37dC and then heat inactivated for 10m at 65dC.
 * J23039 >T9002
 * S03623
 * S03608
 * I13507

Digest for RP-JT and FluorSwitch
I digested the following for 99m99s.

Miniprep (RPJT+FluorSwitch)
I miniprepped the samples that were grown last night: All the nanodrop data was good (about 150 ng/µL with excellent curves), except for the J23039 >T9002 (50ng/µL)
 * For RP-JT constructions
 * R0011 T9002
 * For switching fluorophores
 * S03623
 * S03608
 * E0240
 * I13507

Colony PCR of RP
I colony PCR'ed the R-P constructs that didn't work out the first time:
 * R0011 T9002
 * For switching fluorophores
 * S03623
 * S03608
 * E0240
 * I13507

Colony PCR of R-PJT
Gel

Clonewell RP and JT
I clonewelled the following things (some are Perry's samples):
 * 1+2B XP
 * JsLO ES (very faint)
 * JsLO SP (very faint)
 * B0015 EX
 * R0051 <P0140 colony #1
 * R0051 <P0340 colony #1
 * R0011 <P0340 colony #2

and then vacufuged them.

Dephosphorylating JT
I dephosphorylated JT with Antarctic Phosphotase (1 hr 37dC) and then heat inactivated at 65dC for 10 min.

Clonewell and Vacufuging the RP and JT parts
I clonewelled the leftovers from the RP and JT digests and then vacufuged and resuspended in 20 µL of nuclease free water. This was done in order to try rebuilding the constitutive tetR+JT construct.

Liquid Cultures of 2 cell system and RFP+JT
I grew liquid cultures of the 2 cell system and the RFP+JT in preparation for plate reader experiments tomorrow.

Sequencing the RFP+JT part
I prepared the RFP+JT part and sent it for sequencing.

Sequencing Results

Colony PCR of the tetR+JT constructs Part II
I chose only non-fluorescent colonies (by checking the colonies under the fluorescent microscope) for this colony PCR.

Results: None of the colony PCR's gave the correct size DNA piece.

Gel

Miniprep the RFP+JT
I miniprepped the RFP+JT sample (originally for transformation in Top10 because BL21 expresses LacI, but we decided that we liked the idea of inducible RFP).

Liquid Cultures
I grew liquid cultures of the "correct" RFP+JT colony resulting from the colony PCR.

Colony PCR of the tetR+JT and RFP+JT constructs
I colony PCR'ed the teR+JT and RFP+JT constructs.

Results: Only one colony seemed correct. It was one of the constitutive RFP+JT parts.

Gel

Ligation and Transformation of tetR-JT and RFP-JT constructs
I Roche ligated the following:
 * (R0051 <P0140) <(J23039 <T9002)
 * J04450 <(J23039 <T9002)

and then transformed them into BL21.

Ligation Protocol Transformation Protocol

Clonewell and Vacufuge of the R-P constructs
I clonewelled and vacufuged the R-P constructs and the JT. Unfortunately, I forgot to include the JT with the initial clonewell, so I ended up having to fish the very nasty clonewell out of the garbage (there was a piece of gel on it and chunks of gel were stuck in some of the wells). I used the last two wells (which were thankfully somewhat clean) for ladder and the JT. Unfortunately I ran into a few problems. First, the JT is about 2800 bp and the plasmid is about 2000 bp. The two bands on the clonewell were pretty close and it was difficult to separate the two bands sometimes. Second, the gel stopped running after a while. I noticed bubbles forming along the edges of the gel and whenver I pressed "Go," the gel would make an unhappy beeping noise and blink yellow, so I just stopped running the clonewell

Protocol

Dephosphorylating the R-P constructs
I then incubated at 37dC for 1 hour and heat inactivated at 65dC for 10 minutes.

Protocol

Sequencing the R-P constructs
I prepared and sent off reaction mixes. A summary of the order below:

Sequencing Results

Digesting JT and R-P constructs
I digested the following for 99:99 minutes:

Miniprep and Nanodrop of JT and the R-P constructs
I miniprepped the following parts:
 * R0011 <P0340 colony #2
 * R0051 <P0140 colony #1
 * R0051 <P0340 colony #1
 * R0052 <P0140 colony #2 Lower Right
 * R0052 <P0340 colony #1 Upper Right
 * J23039 <T9002
 * 5
 * 8

The "5" and "8" were Perry's samples. Note that the R0052 <P0340 colony #1 Lower Right is missing. That is because the overnight culture didn't seem to grow. After centrifuging several times, there was still no pellet, so I just tossed that sample out.

The Nanodrop results (after Nanodropping, I made the following dilutions for sequencing samples):

Miniprep Protocol Nanodrop Protocol

Liquid Cultures
I grew up liquid cultures of the following constructs, which come from the colony PCR's that Stephanie did in the morning:
 * R0011 <P0340 colony #2
 * R0051 <P0140 colony #1
 * R0051 <P0340 colony #1
 * R0052 <P0140 colony #2 Lower Right
 * R0052 <P0340 colony #1 Upper Right
 * R0052 <P0340 colony #1 Lower Right
 * J23039 T9002. I also heat inactivated at 65dC for 15 minutes.

After doing this, I was informed by Perry that I shouldn't dephosphorylate the insert. ARGH! I'll need to regrow, miniprep, and digest the JT.

Protocol

Sequencing R0011, R0051, R0052
I prepared the R0011, R0051, and R0052 for sequencing. They are AV09, AV10, and AV11 respectively. Stephanie and I dropped them off in the mailbox.

Sequencing Results

Double Digest of J04450 and JT
I used the following digest mixes:
 * J04450
 * 25 µL DNA
 * 1 µL SpeI
 * 1 µL PstI
 * 0.5 µL BSA
 * 3 µL Buffer 2
 * J23039>T9002
 * 20 µL DNA
 * 1 µL XbaI
 * 1 µL PstI
 * 0.5 µL BSA
 * 2.3 µL Buffer 2

Protocol

Miniprep and Nanodrop of J04450 and JT
I miniprepped and nanodropped the J04450 and the J23039>T9002.

Nanodrop results:
 * J04450 - 91.1 ng/µL
 * J23039>T9002 - 110.8 ng/µL

Miniprep Protocol Nanodrop Protocol

Liquid cultures
I grew up liquid cultures of J04450 and JT in preparation for miniprep, digest, ligation, etc. on Monday 7/16/07.

Transformation of constitutive tetR constructs: Take Two
I transformed the into Top10 and plated on LB carb plates.
 * R0011+P0140
 * R0051+P0140
 * R0052+P0140
 * R0011+P0340
 * R0051+P0340
 * R0052+P0340

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Ligation of P0140, P0340, R0011, and R0051: Take Two
I Roche ligated the following parts:
 * R0011+P0140
 * R0051+P0140
 * R0052+P0140
 * R0011+P0340
 * R0051+P0340
 * R0052+P0340

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Vacufuge of R0011 and R0051: Take Two
There were about .3 mL of water left in the the R0011, R0051, and R0052, so I vacufuged for about 2 hours and then resuspended in 20 µL nuclease-free water.

This was done in preparation for making the constitutive tetR+JT construct.

Clonewell of R0011 and R0051: Take Two
I clonewelled the R0011, R0051, and R0052.

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Dephosphorylation of R0011 and R0051: Take Two
After discovering that the colony PCR's of the BL21 transformations were horrible, Perry decided we should try it again, but dephosphorylate before we clonewell. So I dephosphorylated the R0011, R0051, and R0052 with the following mix:
 * 38 µL DNA
 * 3 µL Antarctic Phosphatase
 * 4.6 µL Antarctic Phosphatase Buffer

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Transformation of constitutive tetR constructs
I transformed the following ligated parts into BL21:
 * R0011 <P0140
 * R0011 <P0340
 * R0051 <P0140
 * R0051 <P0340

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Ligation of P0140, P0340, R0011, and R0051
I ligated the combinations of parts: with the Roche Ligation Kit (the small white box with the tubes numbered 1-3)
 * R0011 <P0140
 * R0011 <P0340
 * R0051 <P0140
 * R0051 <P0340

Protocol:
 * 1) 3 µL vector (R0051 and R0011) + 7 µL insert (P0140 and P0340)
 * 2) Vortex
 * 3) 10 µL Vial 1 (ligation buffer)
 * 4) Vortex
 * 5) 1 µL Vial 3 (ligase)
 * 6) Vortex, Spin down
 * 7) Let stand for 5 min at room temperature

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Dephosphorylation of R0011 and R0051
I treated the R0011 and R0051 with Antarctic Phosphatase. My mix was: I then incubated for 1 hr @ 37dC and heat inactivated for 10 min @ 65dC.
 * R0011
 * 23.2 µL gel extracted R0011
 * 2.7 µL Antarctic Phosphatase Buffer
 * 1 µL Antarctic Phosphatase
 * R0051
 * 22.3 µL gel extract R0051
 * 2.6 µL APB
 * 1 µL AP

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Vacufuge of P0140, P0340, R0011, and R0051
I vacufuged the samples digested on 7/12/07 for a total of about 3 hours. I then resuspended the samples in about 20 µL of nuclease-free water. I nanodropped them, but the numbers were ridiculously high (~200 ng/µL) and the curves looked awful. Note to self: never Nanodrop gel extraction again.

This was done in preparation for making the constitutive tetR+JT construct.

My First Clonewell

 * 1) Get iBase+Clonewell gel. Remove gel (leave the comb!) and place into iBase.
 * 2) Pre-run (Mode 0) for two minutes while the comb is still in the gel
 * 3) Take out comb, load each well in top row with 20 µL samples, the middle well with ~10 µL ladder, and the bottom row wells with 20 µL nuclease-free water
 * 4) Run the gel with (Mode 5: Run Clonewell), watch the bands and stop the gel when your desired band hits the dashed line above the bottom row of wells
 * 5) With the gel stopped, fill the bottom row wells with nuclease-free water.
 * 6) Run the gel again. When you see the band starting to enter the well, take out the sample in the well and put into clean labeled centrifuge tube. Then refill the well with 20 µL nuclease-free water and continue running the gel.
 * 7) Repeat this procedure until you get enough sample. If the band runs past the well, you can use Mode 6: Reverse Clonewell to make the band move back into the well

So basically, I did this for the stuff that was digested (see immediately below) and I ended up with a lot of water, so I am going to vacufuge the results tomorrow.

This was done in preparation for making the constitutive tetR+JT construct.

Digests of P0140, P0340, R0011, and R0051

 * XbaI and PstI digests
 * P0340
 * P0140
 * SpeI and PstI digest
 * R0011
 * R0051
 * Mixture
 * 42.5 µL DNA
 * 1 µL enzyme 1
 * 1 µL enzyme 2
 * 0.5 µL BSA
 * 5 µL Buffer 2

This was done in preparation for making the constitutive tetR+JT construct.

Protocol

Perry's E-gel
I ran an E-gel for Perry's colony PCR.
 * 1) Take out E-gel (leave comb in) and put in one of the bases. NOTE: One of the red bases has a faulty contact which requires covering by aluminum foil to work correctly.
 * 2) Pre-run the gel for 2 minutes. (Press and hold either 15min or 30min on the red bases or Mode 0 on the gray bases)
 * 3) When the pre-run is finished, press any button to stop the beeping.
 * 4) Load 10 µL of nuclease-free water and 10 µL of ladder into the first well. Then 10 µL nuclease-free water + 10 µL sample into every other well. If there are empty wells, put in 20 µL of nuclease-free water into the empty wells. NOTE: Nick mentioned this and it is a pretty good idea. Put the ladder in the middle well or if there are empty wells, put ladder in the end empty wells. This way, it is easier to compare, especially if the bands bend.
 * 5) Run the E-gel for 30-min (Press 30min on the red bases, or run Mode 1 - changing the time if necessary)
 * 6) When the run is done, press any button to stop the beeping. Use the UV machine in the small room to visualize the gel.

It confirmed that P0140 and P0340 were correct. However, I don't think his GFPmeks turned out very well.

Results

Sequencing
I sent out the following for Genewiz sequencing:

The plan was to dilute the above samples to about 40-60 ng/µL and I did the dilutions, but I stupidly ended up using the stock instead of the dilution so our samples had a LOT more DNA than we had planned. Eh, it still ended up working out.

Protocol

Order Summary:

Sequencing Results ---

7/10/07
Colony PCRs

Growing Liquid Cultures of Tomorrow's Plate Reader Samples
Protocol

Stephanie and I grew liquid cultures of the following parts: Also, Stephanie left the T9002 (+) sample incubating with 1000 nM OHHL to serve as a comparison to J37015.
 * I13263
 * I13273
 * I5311
 * I13522
 * B0015
 * T9002 (+)
 * T9002 (-)

Colony PCR of Ligated Parts
Protocol

Stephanie, Perry, and I colony PCR'ed the parts that they ligated the week before.

See Stephanie's notebook for results.

FACS-related
Since each of these were about 2 mL samples, we didn't have enough sample to have 2 mL cuvette samples. Instead, we used 1mL of cells with 10.5 uL HSL. 2 samples were taken from the 1:40 first dilution (8:30am) - used for the 10 and 100nM HSL runs - and 1 from the 1:80, used with 1nM HSL.
 * 8:30 AM - Stephanie and I took the OD of the overnight cultures.
 * Results - 1.785, 1.793, 1.780
 * 9:15 AM - Stephanie and I performed first dilution (growing the 4 hr induction cells). Unfortunately, we didn't dilute correctly...
 * 1:40 dilution: 50 µL liquid culture + 148 µL LB broth + 2 µL ampicillin
 * 1:80 dilution: 25 µL liquid culture + 173 µL LB broth + 2 µL ampicillin
 * 1:100 dilution: 20 µL liquid culture + 178 µL LB broth + 2 µL ampicillin
 * 10:30 AM - Oopsie, we realized we didn't dilute 1:40, etc.; instead, we had actually diluted 1:4, etc. We measured the OD's of these incorrectly diluted samples and rediluted the samples. Note that in order to measure the OD, we diluted samples 1:100, measured the OD, and multiplied the measured OD by 100 to give us our measurement for the actual sample.
 * 1:4 sample OD = 3, redilute 1:100 giving us a sample of about OD=0.03
 * 1:8 sample OD = 1.8, redilute 1:30 giving us a sample of about OD=0.05
 * 1:10 sample OD = 1.3, redilute 1:100 giving us a sample of about OD=0.01
 * Also, we diluted 1:40, 1:80, and 1:100 2 mL samples from the overnight stock to grow as our 2 hr induction cells
 * 11:00 AM - I diluted the stock solution 1:10,000 and 1:1,000,000 in 100 µL 200-proof ethanol to give a 97 µM and 97 nM solution.
 * 11:30 AM - Stephanie and I diluted 1:40, 1:80, and 1:100 2 mL samples from the overnight stock to grow as our 1 hr induction cells
 * 12 noon - Stephanie and I took the OD of the 4 hr induction cells
 * 4 hr induction cells, 1:40: 0.2
 * 4 hr induction cells, 1:80: 0.2
 * 4 hr induction cells, 1:80: 0.1
 * 1:30 pm - Took OD of the 1hr and 2hr samples + Induce the 2 hr samples

See Stephanie's entry for the rest

Transformation and Liquid Culture of Assorted BioBricks
Transformation Protocol

Liquid Cultures Protocol

Perry and I transformed and prepared liquid cultures of the following parts:
 * S03623
 * S03608
 * J37034
 * J23039
 * R0011
 * R0140
 * T9002
 * B0015
 * R0051

Resuspending the HSL stock
I took the 25 mg of N-Butyryl-DL-homoserine lactone and resuspended in 1.5 mL of 200-proof ethanol. I then put the tube in the Quorum sensing box in the freezer at Stephanie's bench.

This was done in preparation for inducing the FACS samples on 6/29/07.

Digestion of F1610: Part Two
Stephanie ran another F1610 digest with
 * 1) 2.5 µL Buffer 2
 * 2) 0.5 µL BSA
 * 3) 0.5 µL XbaI
 * 4) 0.5 µL PstI
 * 5) 21 µL F1610

Basically it is the same as the previous digestion except we now have 21 µL vs. 15 or 6 µL of DNA. This was done because the Clonewell of the F1610 that Perry and I ran had an almost invisibly faint band corresponding to the F1610. Where did all the DNA go?

Grow Liquid Cultures of I13263
Protocol

Stephanie and I grew I13263 in preparation for the FACS on 6/29/07.

Sequences
Perry checked the sequences that we got back from Genewiz Results !!!!upload the sequences?
 * F1610 (something is very wrong...)
 * The actual part is 798 bp, we got back a sequence ~300 bp
 * The sequence contains the terminator and some random junk after it
 * I13263 (w00t)
 * The first and last ~650 bp are perfect.
 * I13273
 * !!!!add something here

Clonewell of F1610
[User:GeorgeXu#My_First_Clonewell Protocol]

Results

F1610 is about 800 bp. There is an almost invisibly faint band at 800 bp. What happened to all the DNA? We need to run it again

Transformation of Additional Parts
Protocol

Perry and I transformed the following parts


 * R0040
 * R0051
 * R0011
 * E0240
 * B0015
 * T9002

Digestion of F1610 (XbaI, PstI)
Mix 1: Mix 2:
 * 1) 2.5 µL Buffer 2
 * 2) 0.5 µL BSA
 * 3) 0.5 µL XbaI
 * 4) 0.5 µL PstI
 * 5) 15 µL F1610 (168 ng/µL)
 * 6) 6 µL Nuclease-free water
 * 1) 2.5 µL Buffer 2
 * 2) 0.5 µL BSA
 * 3) 0.5 µL XbaI
 * 4) 0.5 µL PstI
 * 5) 15 µL Nuclease-free water
 * 6) 6 µL F1610 (168 ng/µL)

Perry and I ran two digests of F1610 with different amounts of DNA. The plan is to gel extract and ligate with the promoters that Perry has transformed.

Protocol

Sequencing the Midiprepped QS parts
Protocol

Just checking if the Midiprepped sequences are correct. Details of the order:

Sequencing Results

Transformation of I13263
Protocol

Stephanie and I transformed 1 µL of the I3263 that we midiprepped into 30 µL of BL21. We then plated them onto agar+ampicillin plates. We eventually want to carry out a test experiment by inducing the I3263 with different concentrations of HSL to test and possibly start characterizing the part.

Hispeed! Midiprepping of the QS parts
Protocol

Perry and I Midiprepped the QS parts in order to get DNA that we could sequence and transform.

Growth of QS parts in Liquid Cultures
Protocol

We grew the QS parts in a liquid LB+ampicillin broth.

Nanodrop
Protocol

Results 10mer: 389.8 ng/µL 15mer: 278.6 ng/µL 20mer: 168.7 ng/µL

Nucleotide Removal of the 10mer, 15mer, and 20mer library
Again, this was done in preparation for the ligation reaction that we will do with the massive amounts of DNA.

Protocol

PCR Extension of the 10mer, 15mer, and 20mer library
Basically, this was done in preparation for the ligation reaction that we will do with the massive amounts of DNA.

Protocol

Transforming and Plating the QS parts
Protocol

Perry transformed the parts F1610, I13263, and I13272 into Top10 cells and plated them on LB+ampicillin plates. We want to sequence the parts, test them, and eventually use them in our BL21 cells.

Counting colonies: Overnight vs. Short Ligation
We counted the number of colonies in the Overnight vs. Short Ligation plates. Results

Nanodrop of Ligated Colonies
Protocol

Results OmpA1+random library+extension: 50.8 ng/µL OmpA2+random library+extension: 50.7 ng/µL The curves looked smooth. %

Protein Gel of OmpA+His/OmpA+Strep Cells
Protocol

We ran this protein gel to see if the OmpA1+His, OmpA1+Strep, OmpA2+His, and OmpA2+Strep was actually expressed. Also, we wanted to see if there was any difference between the immediate induction, delayed induction, and no induction.

Results

Bacterial Innoculation and Induction
Inocculation and Induction Protocol

Measuring Optical Density Protocol

We took the OmpA1+His, OmpA1+Strep, OmpA2+His, and OmpA2+strep that were grown in liquid culture overnight starting on 6/20/07 and split them into three sets. The first set was not induced, the second set was immediately induced with 10 µL IPTG¸ and the final set was induced once it hit log phase, which we determined by measuring the optical density.

Optical Density Results

Gel Extraction
Protocol

We extracted the DNA from the gel we ran on 6/19/07

Gel after Excision

Running the OmpA1/OmpA2 gel
Protocol

We poured a gel and ran the DNA from the dephosphorylated samples.

Results

Dephosphorylating the OmpA1/OmpA2
Protocol

Six times this amount of mix was made as a Master Mix in order to dephosphorylate the OmpA1 and OmpA2. There were five groups total:
 * 1) Group 1: OmpA1, Nhe1, Pst1
 * 2) Group 2: OmpA1, Nhe1, Pst1
 * 3) Group 3: OmpA2, Nhe1, Pst1
 * 4) Group 4: OmpA2, Nhe1, Pst1
 * 5) Group 5: Perry...