Bacterial Pest attractor (engineer bacteria to produce a substance, such as a pheromone or smell, that attracts and kills pests such as insects).
Natural pesticides (engineer bacteria to produce a substance that repels or kills pests, such as those that harm crops, that can later be implemented into plants).
Water/Environment
Desalination of water (engineering bacteria to get rid of salt in salt water in order to make drinkable water from sea water).
Getting rid of estrogen mimicking compounds in water (engineering bacteria to degrade them or sequester them)
Waste treatment (engineering bacteria that can be integrated into waste water treatment).
CFCs (engineer bacteria to produce metabolites that break down chlorofluorocarbons—compounds that contribute to the degradation of the ozone layer).
Health
Stomach ulcers (creating a medication containing engineered bacteria to specifically target and kill Helicobacter pylori – the organism that causes stomach ulcers).
Diabetes (engineered bacteria as Islet cells to produce insulin).
Allergies/Immune system (engineer bacteria to produce antihistamines or alter epitopes).
Bone density (engineer bacteria to produce and secrete calcium and other compounds to help heal broken bones or to prevent osteoporosis).
Process Improvement
Oil fractionation catalyst (engineering bacteria to improve the separation of crude oil into valuable fraction and waste fraction).
Nitrate fixation (engineer bacteria to improve nitrogen fixation so not as much fertilizer is needed).
Kill Switches
Engineering bacteria to undergo induced or programmed cell death in order to control the organism).
The chosen project
After dividing in to a few groups based on which project was preferred, each group made a presentation on the proposed project. In the end, we decided to go with the glucose sensing project.
Project outline
Possible things to consider:
Glucose and insulin
Detection of blood glucose levels (glucose-specific promoter?)
Insulin production release (measure/regulation of production?)
Immune response
Possibly use "bactoblood" strain from Berkeley 2007
Kill switch
Control and
Delivery system
Intravenous
NASA Biocapsule
April
Sub-groups
We divided the team into sub-groups. Each group assumed responsibility for a different aspect of the project.
Wiki and Mascot Design
This group is responsible to obtaining and uploading all necessary information to the wiki. This includes team pictures and biographies, experiments and results, and the projects of the other sub-groups. This will be a priority over mascot design.
This group is responsible for letting the public know what our team is and what we are doing. This can be done creatively. The point is to raise awareness for iGEM, synthetic biology, and diabetes.
Leader: Chris Isaac
1. Shammamah Hossain
2. Dawson Meyer
3. Yoyo Yao
4. Jared Sparkes
5. Wesley Mosimann
6. Trisha Bouma
7. Janelle Veenendaal
8. Orion Sehn
WHMIS tests and Safety Training
We are required to have safety training in order to work in the lab, and so we all wrote our WHMIS tests and did our Hazards Assesment and lab orientation!
May
May 8, 2012: Tansformation of Parts from Kit Plate and Growing Cells from Glycerol Stocks
Transformation of parts from kit plate:
B0034 in pSB1A2
K093005 in pSB1A2
J23100 in J61002 (Amp)
E1010 in pSB2K3
Overnight cultures were also made of:
pMA-T K33109 (HST-1)
pSB1AK3 B0014
May 9, 2012: Miniprep and Restriction of Parts
Overnight cultures from May 8th were miniprepped and restricted in order to determine sizes.
Master mix was prepared by mixing the ingredients together in order, as shown above. 20µL worth of master mix was combined with 5µL of plasmid DNA:
pMA-T BBa_K331009 (Heat-stable toxin signal sequence)
pSB1AK3 BBa_B0014 (Double terminator)
Restrictions were incubated at 37˚C for 30mins then stored at -20˚C.
Colonies were also picked. Overnight cultures were made of :
E1010 pSB2K3
J23100 J61002 (Amp)
K93005 pSB1A2
B0034 pSB1A2
May 10, 2012: Miniprep and Restriction of Parts
Overnight cultures from May 9th were miniprepped and restricted in order to determine sizes
Master mix was prepared by mixing the ingredients together in order, as shown above. 20µL worth of master mix was combined with 5µL of plasmid DNA (1-7).
J23100 (J61002)
J23100 (J61002)
B0034 (pSB1A3)
B0034 (pSB1A3)
E1010 (pSB2K3)
E1010 (pSB2k3)
K093008 (pSB1A2)
Restrictions were incubated at 37˚C for 30min then stored in -20˚C.
May 11th: Electrophoresis of restricted parts from May 10th
Purpose: confirm existence of the following parts:
J23100 (J61002)
B0034 (pSB1A3)
E1010 (pSB2K3)
K093008 (pSB1A2)
We also grew up J04500 in pSB1AK3 for assembly
PCR of RFP (E1010) into fusion standard
(adding extra bp to get into fusion standard)
Add 17.8 uL to 8 tubes with:
Pfu polymerase 0.2 uL
Template DNA 2 uL
Put tubes on gradient function program Pfu test with various annealing temperatures:
Annealing gradient (degrees celsius):
49.2
51.6
53.0
54.5
55.9
57.3
58.8
61.2
only 54.5 worked
May 12th: Assembly of promoter & RBS (J04500) with signal sequence (K331009) and RPF (E1010 fusion) with double terminator (B0015)
Method: Restriction, gel extraction, and ligation
Restriction:
J04500
K331009
E1010 (fusion)
B0015
Gel extraction:
We made a 1% TAE agarose gel and ran restrictions for 1 hour @ 120V
We then gel extracted the DNA
Ligation:
Ligated together J04500 & K331009
Ligated together E1010 fusion & B0015
May 13th Transformation of ligated products: J04500 + K331009 and E1010 (fusion) + B0015
Transformation:
2uL of each ligation mix was added to 20uL DH5ɑ cells
Incubated on ice for 30 mins
Cells were then heat shocked for 45sec in water bath at 42 degrees Celsius
Immediately after, cells were incubated on ice 5 mins
400uL SOC media was added and cells were resuspended
Cells were then placed in shaker for 1h @ 37 degrees
200uL of this culture was plated on AMp plates
Plates were incubated at 37 degrees for appx. 16h
May 14th: Picking Cells from May 13th transformation
Cells grew on 2 plates, 2 colonies were picked
Picked cells were put into 5ml LB media with kanamycin
Cells did not grow
May 19th: PCR of E1010 and J23100 (Mlc primers)
E1010:
Add 49.5uL to 4 PCR tubes and add 0.5uL Taq polymerase and 1uL template DNA to each
E1010 (fusion) primer annealing temp – 55.5˚C
J23100:
Add 49.5 uL of MM to 4 PCR tubes and add 0.5 uL Taq polymerase to each tube
J23100-Mlc primer annealing temp- 58.0˚C
Ran 1.5% agarose TAE gel at 90V for 45 mins
E1010 expected size: 700 bp
J23100 expected size: 215 bp
Did not work
May 20: Re-do May 19 PCR of E1010 (fusion) and J23100-mlc
Alterations to PCR:
2uL MgCl2
PCR cycle:
First Denaturation: 3 mins @ 94˚
Denaturation: 15 sec @94˚
Annealing: 30sec E1010: 54.5˚ J23100: 55.0˚
Elongation: I min 30 sec @ 72˚
Final elongation: 7 mins @72˚
Add 49.5 uL of MM to 4 PCR tubes
Add 1uL template DNA
Add 0.5 uL Taq DNA polymerase to each
Didn’t work (again!)
May 21st: PCR of J23100 and E1010 repeat again!
For both J20100 and E1010*:
Put 45.9 uL of MM into x PCR tubes
Add 3 uL of template DNA
PCR PFU test #4
Ran on 1.5% agarose gel at 120V for 1hour
PCR protocol:
First Denaturation: 2 mins @ 95˚
Denaturation: 30 sec @95˚
Annealing: 30sec E1010: 54.5˚ J23100: 55.0˚
Elongation: I min 30 sec @ 72˚
First elongation: 7 mins @72˚
changed to 30 cycles
May 22, 2012: PCR of J23100-Mlc
PCR Parameters:
Initial denaturation 95˚C 3mins
30 cycles of:
*denaturation 95˚C 30s
*annealing (various) 30s
*elongation 72˚C 1min
Final elongation 72˚C 7mins
PCR Samples:
PCR product expected size: 214 bps
1.5% agarose gel
Ran at 120v for 1 hr
May 23, 2012: Ligation of PCR products into pGEM Vector
1) prefix –J23100-mlc-spe cut site (Red tubes) (sample 3 from May 22nd PCR)
2) Prefix-(fusion)-E1010-suffix (Black tubes) (sample 1 from May 23rd PCR)
Contents:
2x Rapid Ligation Buffer 5µL
pGEM-Tor pGem-T Easy Vector 1µL
PCR Product 3 µL
T4 DNA Ligase 1µL
MiliQ H2O 1 µL
Ligate at room temp for 1h 15 mins
One of each sample ligated overnight @ 4˚c
2 of each ligated at room temperature for approx. 1hr
May 23, 2012 Transformation of J23100-Mlc and E1010 fusion
For each ligation mix:
Added 2µL of ligation mix ( E1010 pcr + pGEM; J23100- mlc + pGEM) to 20.0µL of DH5α)
Incubated on ice for 30mins
45secs in water bath @ 42˚C
immediately incubated on ice for 5mins
Added 400µL of SOC media; resuspended
Put in shaker for 1hr @ 37 ˚C
200µL cultured onto plate(4 plates, Amp)
Incubate @ 37 ˚C for approximately 16hrs
May 23rd continued
Make: 1.5% agarose gel
-0.45 agarose M
-30 mL TAE (1x)
Run PCR samples 1, 3, & 4 from PCR (E1010 RFP)
Add 100bp ladder to two lanes
Middle three lanes ass 5uL of PCR product
Run at 120V for 1 hour
May 24, 2012: Transformation of PCR Products in pGEM Vectors in DH5ɑ
Sample 3 from PCR product ligation
For each ligation mix:
Added 2µL of ligation mix ( E1010 pcr + pGEM; J23100- mlc + pGEM) to 20.0µL of DH5α
Incubated on ice for 30mins
45secs in water bath @ 42˚C
immediately incubated on ice for 5mins
Added 400µL of SOC media; resuspended
Put in shaker for 1hr @ 37 ˚C
200µL cultured onto plate(4 plates, Amp)
Incubate @ 37 ˚C for approximately 16hrs
May 24 picking colonies of J20100-mlc and E1010 in DH5ɑ
For each sample:
Pipette 5 uL of ampicillin into 5 mL LB media
Pick colony from plate with a pipette tip and eject tip into media
Shake at 37⁰C for approx. 8h
May 25, 2012: QIA Spin Miniprep of J23100-mlc (A: colony 1), J23100-mlc (B: colony 2)
Put 1.5mL of transformed cells in a microcentrifuge tube; centrifuge and repeat until cells from entire tube are in the microcentrifuge tube.
Resuspend pelleted bacterial cells in 250uL Buffer P1
Add 250uL Buffer P2, mix by inversion
Add 350uL Buffer N3, mix by inversion
Centrifuge for 10 mins @ 13000 rpm
Put supernatant into the QIAprep spin column
Centrifuge for 60s at 14000 rpm, discard flow through
Add 750uL buffer PE and centrifuge for 60s at 14000 rpm
Centrifuge again to get rid of remaining buffer
Add 50uL of Buffer EB to spin columns, let stand for I min, centrifuge for 1 min at 14000 rpm
May 26 gel of Miniprep samples
Gel run to check miniprep samples for DNA
Ran at 120V for 60 minutes
May 29, 2012: Transformation of E1010 fusion in pGEM in DH5ɑ
For each ligation mix:
Added 2µL of ligation mix ( E1010 pcr + pGEM; J23100- mlc + pGEM) to 20.0µL of DH5α
Incubated on ice for 30mins
45secs in water bath @ 42˚C
immediately incubated on ice for 5mins
Added 400µL of SOC media; resuspended
Put in shaker for 1hr @ 37 ˚C
200µL cultured onto plate(4 plates, Amp)
Incubate @ 37 ˚C for approximately 16hrs
May 30 QIA spin Miniprep
DNA:
E1010 psB2k3
E1010 fusion pGEM
J20100-mlc pGEM
CK331009 psEk3
E1010 p5B2k3
Put 1.5mL of transformed cells in a microcentrifuge tube; centrifuge and repeat until cells from entire tube are in -the microcentrifuge tube.
Resuspend pelleted bacterial cells in 250uL Buffer P1
Add 250uL Buffer P2, mix by inversion
Add 350uL Buffer N3, mix by inversion
Centrifuge for 10 mins @ 13000 rpm
Put supernatant into the QIAprep spin column
Centrifuge for 60s at 14000 rpm, discard flow through
Add 750uL buffer PE and centrifuge for 60s at 14000 rpm
Centrifuge again to get rid of remaining buffer
Add 50uL of Buffer EB to spin columns, let stand for I min, centrifuge for 1 min at 14000 rpm
June
June 1, 2012: Restriction of J23100-Mlc, K093005, B0014 (samples 1 and 2), K331009_PSB1C3, K331009, E1010 Fusion (samples 1 and 2), J04500
Gel Extraction
Only J04500 (lane 6) and K331009 (lane 9) were the expected size
Restrictions were incubated at 37˚C for 30min then stored in -20˚C
June 2, 2012: Miniprep of June 1 Cultures
Transfer 1.5mL of cell culture to microcentrifuge tube; centrifuge at 5000xg for 2 minutes. Repeat three times.
resuspend pelleted cells in 250 µL of Buffer P1
add 250 µL of buffer P2 and mix by inversion
add 350 µL of Buffer N1 and mix by inversion
centrifuge for 10 minutes at 10000 rpm
apply supernatant to the QIAspin column by decanting
centrifuge at 13000 prm for 30 seconds
wash column by adding 0.75 mL of Buffer PE and centrifuging at 13000 rpm for 30s
discard flow through and centriguge for an additional mintue to remove residual buffer
to elute DNA, place column in a microcentrifuge tube, add 50 µL of Buffer EV to centre of column, let stand for 1 minute, centrifuge for 1 minute
results?
June 3, 2012: Confirmaiton of Parts
What worked:
B0015_PSBIAK3
K331009_PSBIC3
J04500_PSBIAK3
B0015_PSBIAK3
J04500_PSBIAK3
B0015 _PSBIAK3
June 4, 2012: PCR to Confirm J23100-Mlc in pGEM
Add 17.8 µL of the Master Mix to four microcentrifuge tubes.
Add the template DNA and Pfu polymerase.
Transformation of TAT-E1010_pGEM (x2) and J23100-Mlc_pGEM (x1) into DH5α
For each ligation mix:
Added 2µL of ligation mix ( E1010 pcr + pGEM; J23100- mlc + pGEM) to 20.0µL of DH5α
Incubated on ice for 30mins
Incubated 45secs in water bath @ 42˚C
immediately incubated on ice for 5mins
Added 400µL of SOC media; resuspended
Put in shaker for 1hr @ 37 ˚C
200µL cultured onto plate(4 plates, Amp)
Incubate @ 37 ˚C for approximately 16hrs
June 5, 2012: Transformation of J06702 (mCherry RFP) into DH5α
Add 10µL of MilliQ H2O into Kit Plate (Spring 2011, Kit Plate #2, well E8)
Added 2µL of DNA to 20.0µL of DH5α
Incubated on ice for 30mins
Incubated 45secs in water bath @ 42˚C
immediately incubated on ice for 5mins
Added 400µL of SOC media; resuspended
Put in shaker for 1hr @ 37 ˚C
200µL cultured onto plate(4 plates, Amp)
Incubate @ 37 ˚C for approximately 16hrs
Gel Extraction of June 4 Restrictions
June 6, 2012: Gel of J23100-Mlc_pGEM Restriction (June 4)
Sample B worked
Miniprep of J06702
Gel confirming J06702 miniprep
Conformation of part BBa_J06702
Miniprep sample cut with EcoR1 and ran on a 1% agarose gel at 120V for 50 mins
Lanes 4, 5, and 6 contain restricted J06702 in pGEM
Put 1.5mL of transformed cells in a microcentrifuge tube; centrifuge and repeat until cells from entire tube are in the microcentrifuge tube.
Resuspend pelleted bacterial cells in 250uL Buffer P1
Add 250uL Buffer P2, mix by inversion
Add 350uL Buffer N3, mix by inversion
Centrifuge for 10 mins @ 13000 rpm
Put supernatant into the QIAprep spin column
Centrifuge for 60s at 14000 rpm, discard flow through
Add 750uL buffer PE and centrifuge for 60s at 14000 rpm
Centrifuge again to get rid of remaining buffer
Add 50uL of Buffer EB to spin columns, let stand for I min, centrifuge for 1 min at 14000 rpm
3 samples were made and ran on a gel, all samples appeared to be the expected size
PCR of E1010 Fusion (to confirm part) and TAT-E1010 (for insertion into pGEM)
Add 18.8 µL of the Master Mix into 4 microcentrifuge tubes
Add E1010 Fusion and Pfu polymerase
TAT-E1010 PCR for insertion into pGEM gel
PCR of TAT-E1010 with Taq polymerase
Lanes 4, 5, 6 contain the PCR product to be inserted into pGEM
1Kb ladder in lane 9
Add 24.25 µL of the Master Mix into 4 microcentrifuge tubes
Add TAT-E1010 and Taq polymerase
Size Confirmation Gel of E1010 fusion, TAT-E1010, J23100-Mlc, J04500
All TAT-E1010 samples worked
Sample from lane 5 was ligated with pGEM
June 7th 2012
Transformation
2x TAT-E1010(pGem) Amp.
1xJ23100-mlc(pGem) Amp.
Added 2.0 microlitres, mixed to 20 microlitres of DH5 Alpha.
Incubated on ice for 30 minutes.
Placed in water bath for 45 seconds at 42 degrees Celsius.
Immediately incubated in ice for 5 minutes.
Added 400 microlitres of SOC media, re-suspended.
Shaked for one hour @ 37 degrees Celsius.
While shaking, 40ul of 0.1M IPTG and 40ul X-Gal was added to each plate
Added 200 microlitres onto plate.
Incubated for approximately 16 hours at 37 degrees Celsius.
June 9th 2012
Restriction (X, P) and gel extraction of TAT-E1010
Ligation of TAT-E010 with previously gel-extracted J04500 in pSB1AK3 (s,p)
June 10th 2012
Restriction of J23100-mlc with E and X and J06702 with S and P
Ligation of J23100-mlc with J06702 (pSB1A2)
Samples A and B were J23100-mlc (gel extracted from June 10th) + J06702
Samples C and D were J23100-mlc (normal restrictin) + J06702
June 11th 2012
Transformation of J23100-mlc-J06702 samples from June 10th according to standard protocol
4 plates (according to June 10th ligation):
A
B
C
D
2x J23100-m/c (gel extraction) Amp.
2x J06702 Amp.
Added 2.0 microlitres, mixed to 20 microlitres of DH5 Alpha.
Incubated on ice for 30 minutes.
Placed in water bath for 45 seconds at 42 degrees Celsius.
Immediately incubated in ice for 5 minutes.
Added 400 microlitres of SOC media, re-suspended.
Shook for one hour @ 37 degrees Celsius.
Added 200 microlitres onto plate.
Incubated for approximately 16 hours at 37 degrees Celsius.
June 12th 2012
Picking cells:
Colonies grew on all 4 plates
Cells were picked from each plate and put into 5ml LB flasks with 5ul Ampicillin each
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