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- | {|style="color:#1c2bf2;background-color:#fafa19;font-size:9pt;text-align:center" cellpadding="5" cellspacing="0" border="1" bordercolor="#fff" width="62%"
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- | !
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- | |Sunday
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- | |Monday
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- | |Tuesday
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- | |Wednesday
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- | |Thursday
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- | |Friday
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- | |Saturday
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- | !Week 1
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- | |[[Team:Michigan/Oil_Sands#6/28/2010|6/28/2010]]
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- | |[[Team:Michigan/Oil_Sands#6/29/2010|6/29/2010]]
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- | |[[Team:Michigan/Oil_Sands#6/29/2010 and 6/30/2010|6/30/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/1/2010|7/1/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/2/2010|7/2/2010]]
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- | !Week 2
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- | |[[Team:Michigan/Oil_Sands#7/7/2010|7/7/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/8/2010|7/8/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/9/2010|7/9/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/10/2010|7/10/2010]]
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- | !Week 3
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- | |[[Team:Michigan/Oil_Sands#7/12/2010|7/12/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/13/2010|7/13/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/14/2010|7/14/2010]]
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- | | -
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- | !Week 4
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- | | -
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- | !Week 5
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- | |[[Team:Michigan/Oil_Sands#7/25/2010|7/25/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/26/2010|7/26/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/27/2010|7/27/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/28/2010|7/28/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/29/2010|7/29/2010]]
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- | |[[Team:Michigan/Oil_Sands#7/30/2010|7/30/2010]]
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- | |}
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- | ==Oil Sands Lab Notebook==
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| | | |
- | This team includes [[User:annlesn|Ann Lesnefsky]], [[User:rajabiab|Bryce Rajabian]], and [[User:kilholee|Kilho Lee]].
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| | | |
- | ==6/28/2010== | + | ==Oil Sands Lab Notebook== |
- | ''' ''Pseudomonas putida'' KT2440 Antibiotic Resistance'''
| + | |
- | *[[Media:6-28-2010_Protocol_for_making_cultures_from_a_-80C_freezer_stock.pdf|Protocol for starting overnight culture from -80°C freezer]]
| + | |
- | *All protocols can also be found in the ''Protocols'' section of the Notebook
| + | |
- | | + | |
- | ==6/29/2010==
| + | |
- | ''' ''Pseudomonas putida'' KT2440 Antibiotic Resistance'''
| + | |
- | *[[Media:6-29-2010_Making_Frozen_Stoks.pdf|Protocol for making frozen stocks]]
| + | |
- | | + | |
- | ==6/29/2010 and 6/30/2010==
| + | |
- | ''' ''Pseudomonas putida'' KT2440 Antibiotic Resistance'''
| + | |
- | *[[Media:6-27-2010_P._putida_antibiotic_resistance_protocol.pdf|Protocol for ''P. putida'' KT2440 antibotic resistance]]
| + | |
- | | + | |
- | ==7/1/2010==
| + | |
- | ''' ''Literature Review'' Napthenic Acids Composition & HPLC Analysis'''
| + | |
- | *[[Media:6-29-2010_Naphthenic_acids_Composition.pdf|Literature Review of the composition of napthenic acids in oil sands]]
| + | |
- | | + | |
- | ==7/2/2010==
| + | |
- | *[[Media:6-30-10_HPLC_Column_Comparison_Sheet1.pdf|Literature Review of HPLC columns for analysis of napthenic acids]]
| + | |
- | ''' ''Pseudomonas putida'' KT2440 Antibiotic Resistance'''
| + | |
- | *[[Media:7-2-2010_Results_P._putida_antibiotic_resistance.pdf|Results]]
| + | |
- | ==7/7/2010==
| + | |
- | ''Ann''
| + | |
- | | + | |
- | '''Biobrick Transformation''' with Alex and Jennifer
| + | |
- | *Made CaCl2 solution, and 100 mg/mL amphicilin stock solution according to the media section of the wiki
| + | |
- | *Started an overnight culture of DH5alpha according to the heat shock transformation protocol
| + | |
- | **A 12 mL culture was started because we were multiplying the protocol by 4
| + | |
- | | + | |
- | ==7/8/2010==
| + | |
- | ''Ann''
| + | |
- | | + | |
- | '''Biobrick Transformation''' with Marc, Katie and Audra according to the heat shock transformation protocol
| + | |
- | *Started culture for biobrick transformation from over night at 2:30
| + | |
- | *At 5:00pm the cultures had overgrown to an OD600 of 1.2
| + | |
- | **A a 1:3 dilution of cells was performed and the cells were allowed to go through another doubling period of 20 minutes
| + | |
- | *The OD600 was measured again and found to be around 0.500
| + | |
- | *the cultures were placed on ice at 5:30 and allowed to chill for 20 minutes
| + | |
- | *The washings were performed and the comp cells were resuspended in the residual CaCl2 only
| + | |
- | *The OD600 of the comp cells without the glycerol was above 0.3 therefore the comp cells were concentrated enough
| + | |
- | *The heat shock was performed for the following biobricks
| + | |
- | **BBa_179015
| + | |
- | **BBa_179005
| + | |
- | **BBa_145001
| + | |
- | **BBa_117008
| + | |
- | **BBa_117002
| + | |
- | **BBa_103006
| + | |
- | *The cultures were placed in the 30C shaker to grow up for an hour at 30C at 9:00pm
| + | |
- | *The cultures were plated at 10:00pm
| + | |
- | ==7/9/2010==
| + | |
- | ''Ann''
| + | |
- | | + | |
- | '''Biobrick Transformation''' with Josh, Prae, Charlie according to the miniprep protocol
| + | |
- | *After 9 hours of growing at 37C, the plates did not have any colonies on them
| + | |
- | *After 22 hours of growth plates that had grown had clear colonies
| + | |
- | **The positive and negative controls grew out accordingly
| + | |
- | **Only BBa_179015 and BBa_179005 had colonies (both from plate 1 and none from plate 2...)
| + | |
- | ***BBa_179015 had over 100 colonies
| + | |
- | ***BBa_179005 had 2 colonies
| + | |
- | *5 mL overnight cultures were started with 100 mg/mL amp at 8pm from a single colony on each plate
| + | |
- | | + | |
- | ==7/10/2010==
| + | |
- | ''Ann''
| + | |
- | | + | |
- | '''Biobrick Transformation''' with Marcus, Bryce, Kilho, Josh, Charlie, Jeremy
| + | |
- | | + | |
- | Miniprep
| + | |
- | *Made frozen stocks from overnight culture of miniprep
| + | |
- | *Performed miniprep on BBa_179015 and BBa_179005
| + | |
- | *Measured DNA concentration with the Nanodrop
| + | |
- | **BBa_179015-11 ng/mL
| + | |
- | **BBa_179005-40 ng/mL
| + | |
- | | + | |
- | Digest
| + | |
- | *Ran according to the digest protocol in the protocol section
| + | |
- | **Cut parts with EcoRI and PstI
| + | |
- | *Digested at 37C for 30 minutes
| + | |
- | | + | |
- | Gel
| + | |
- | *Ran according to the protocol in the protocol section
| + | |
- | *Used 8 well comb instead of 13 well comb so the samples were too dilute too see
| + | |
- | | + | |
- | ==7/12/2010==
| + | |
- | | + | |
- | ''Ann''
| + | |
- | | + | |
- | '''Biobrick Transformation''' with Jeremy
| + | |
- | | + | |
- | Gel
| + | |
- | | + | |
- | [[Image:7-12-2010_T7_promoter_and_T7_gfp_biobricks.JPG|300px]]
| + | |
- | *Reran gel from 7/10/2010
| + | |
- | **Lane 1-Invitrogen 1 kb plus ladder
| + | |
- | **Lane 2-Digested Bba_179005
| + | |
- | ***Ran out of undigested Bba_179005
| + | |
- | **Lane 3-Digested Bba_179015
| + | |
- | **Lane 4-Uncut miniprep plasmid Bba_179015
| + | |
- | | + | |
- | We found that we successfully extracted BBa_179015, T7-GFP, because there were expected bands at 906 and 2079 as faintly seen in the gel picture above. No appeared for biobrick Bba_179005, T7 promoter, so this biobrick will be transformed again.
| + | |
- | | + | |
- | '''Biobrick Transformation take 2''' with Jeremy
| + | |
- | | + | |
- | Autoclaved DI water for transformation and autoclaved sterile containers
| + | |
- | *to autoclave sterile containers fill with DI water and decant the water before you start the culture in the container
| + | |
- | | + | |
- | ==7/13/2010==
| + | |
- | | + | |
- | '''Biobrick Transformation take 2''' with Jeremy, Marcus, Josh, Kevin, Audra, Katie
| + | |
- | | + | |
- | ''Ann''
| + | |
- | | + | |
- | Performed according to the electroporation transformation
| + | |
- | *Started the culture at 9:05am
| + | |
- | *Removed the culture at 12:05pm with an OD600 of 0.809
| + | |
- | *The OD600 of the comp cells were 1.2 after washing
| + | |
- | *The time constant for all electroporation were between 5.6 and 5.8 for the following biobricks
| + | |
- | **Bba_K117008
| + | |
- | **Bba_K117008 #2 (from resuspending remaining part left in registry in 15 uL of ultra pure water)
| + | |
- | **Bba_K117002
| + | |
- | **Bba_K145001
| + | |
- | **Bba_K103006
| + | |
- | **Bba_I719005
| + | |
- | *The cultures were allowed to grow in the incubator from 2:15-4:00pm
| + | |
- | **The cultures started to clump after growing this time
| + | |
- | *100 uL of cells were plated on 100 mg/mL AMP plates
| + | |
- | | + | |
- | ==7/14/2010==
| + | |
- | | + | |
- | '''Biobrick Transformation take 2'''
| + | |
- | | + | |
- | ''Ann''
| + | |
- | | + | |
- | Electroporation Transformation
| + | |
- | | + | |
- | All of the transformation plates grew out! (minus the negative control of course)
| + | |
- | | + | |
- | This means we should do all transformations by electroporation from now on. Just check with the Lin Lab to make sure we can use the electroporation machine for a few hours before starting
| + | |
- | | + | |
- | Miniprep
| + | |
- | *Started overnight cultures in 5 mL of LB plus 100 mg/mL AMP
| + | |
- | **The following biobricks were started from the transformation plate
| + | |
- | ***Bba_K117008
| + | |
- | ***Bba_K117002
| + | |
- | ***Bba_K145001
| + | |
- | ***Bba_K103006
| + | |
- | ***Bba_I719005
| + | |
- | **The following biobricks were started from the frozen stock in the -80C freezer
| + | |
- | ***BBa_K719015
| + | |
- | | + | |
- | '''INPNC Biobrick part'''
| + | |
- | *We received the INPNC biobrick (Bba_K265008) from UC Davis 2009 team. THANK YOU!!!
| + | |
- | *It was shipped on LB plates in a pMA-SK plasmid from Mr. Gene in ''E. coli'' DH5alpha
| + | |
- | *Since this plasmid has AMP antibiotic resistance I am pouring plates today with Marc and Kevin with 100 mg/mL AMP resistance to streak out the culture tomorrow with Josh
| + | |
- | | + | |
- | ==7/25/2010==
| + | |
- | | + | |
- | '''Biobrick Transformation of suface display and pBAD'''
| + | |
- | | + | |
- | ''Ann''
| + | |
- | | + | |
- | Tonight I started an 8mL culture of E. coli DH5alpha in LB broth and place in the 30C shaker to grow out overnight
| + | |
- | | + | |
- | ==7/26/2010==
| + | |
- | | + | |
- | '''Biobrick Transformation of suface display and pBAD'''
| + | |
- | | + | |
- | ''Ann''
| + | |
- | | + | |
- | Electroporation transformation
| + | |
| | | |
- | Started larger culture for comp cell preparation in 40mL of LB in a 500 mL sterile container at 9:00am
| + | Members of this team include [[User:annlesn|Ann Lesnefsky]], [[User:rajabiab|Bryce Rajabian]], [[User:chillywings|Marcus Lehr]], [[User:Infekt|Alex Pyden]], [[User:Jeremigo|Jeremy Golden]], [[User:Seongkyu|John Seong Kyu Yang]] and [[User:kilholee|Kilho Lee]]. |
| | | |
- | At 11:30am the OD of the culture was 0.730 and the cultures were placed on ice
| + | ==Monthly Notebooks== |
| + | Notebooks are ordered by month. |
| | | |
- | The transformation of the biobricks was performed for according to the electroporation transformation protocol listed under the protocol section
| + | [[Team:Michigan/Oil_Sands_June_July | June/July]] |
| | | |
- | The biobricks removed from the registry are as follows
| + | [[Team:Michigan/Oil_Sands_August_September | August/September]] |
- | *E0040 (GFP)
| + | |
- | *K157013 (linker)
| + | |
- | *
| + | |
| | | |
- | The OD600 of the comp cells were not measured
| + | [[Team:Michigan/Oil_Sands_October | October]] |
| | | |
- | All of the time constants
| + | =='''In the Lab'''== |
- | ==7/27/2010== | + | <html> |
- | ==7/28/2010== | + | <iframe src="http://www-personal.umich.edu/~shanwu/wiki_photos/src/themes/classic/classic-demo.html" width="100%" height="650px" scrolling="no"></iframe> |
- | ==7/29/2010==
| + | </html> |
- | ==7/30/2010==
| + | |