Team:Michigan/Oil Sands

From 2010.igem.org

(Difference between revisions)
 
(11 intermediate revisions not shown)
Line 2: Line 2:
{{Michigan Header}}
{{Michigan Header}}
-
{|style="color:#1c2bf2;background-color:#fafa19;font-size:9pt;text-align:center" cellpadding="5" cellspacing="0" border="1" bordercolor="#fff" width="62%"
 
-
|-
 
-
!
 
-
|Sunday
 
-
|Monday
 
-
|Tuesday
 
-
|Wednesday
 
-
|Thursday
 
-
|Friday
 
-
|Saturday
 
-
|-
 
-
!Week 1
 
-
| -
 
-
|[[Team:Michigan/Oil_Sands#6/28/2010|6/28/2010]]
 
-
|[[Team:Michigan/Oil_Sands#6/29/2010|6/29/2010]]
 
-
|[[Team:Michigan/Oil_Sands#6/29/2010 and 6/30/2010|6/30/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/1/2010|7/1/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/2/2010|7/2/2010]]
 
-
| -
 
-
|-
 
-
!Week 2
 
-
| -
 
-
| -
 
-
| -
 
-
|[[Team:Michigan/Oil_Sands#7/7/2010|7/7/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/8/2010|7/8/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/9/2010|7/9/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/10/2010|7/10/2010]]
 
-
|-
 
-
!Week 3
 
-
| -
 
-
|[[Team:Michigan/Oil_Sands#7/12/2010|7/12/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/13/2010|7/13/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/14/2010|7/14/2010]]
 
-
| -
 
-
| -
 
-
| -
 
-
|-
 
-
!Week 4
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
|-
 
-
!Week 5
 
-
|[[Team:Michigan/Oil_Sands#7/25/2010|7/25/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/26/2010|7/26/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/27/2010|7/27/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/28/2010|7/28/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/29/2010|7/29/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/30/2010|7/30/2010]]
 
-
|[[Team:Michigan/Oil_Sands#7/31/2010|7/31/2010]]
 
-
|-
 
-
!Week 6
 
-
|[[Team:Michigan/Oil_Sands#8/1/2010|8/1/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/2/2010|8/2/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/3/2010|8/3/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/4/2010|8/4/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/5/2010|8/5/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/6/2010|8/6/2010]]
 
-
| -
 
-
|-
 
-
!Week 7
 
-
|[[Team:Michigan/Oil_Sands#8/8/2010|8/8/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/9/2010|8/9/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/10/2010|8/10/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/11/2010|8/11/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/12/2010|8/12/2010]]
 
-
| -
 
-
|[[Team:Michigan/Oil_Sands#8/14/2010|8/14/2010]]
 
-
|-
 
-
!Week 8
 
-
| -
 
-
|[[Team:Michigan/Oil_Sands#8/16/2010|8/16/2010]]
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
|-
 
-
!Week 9
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
|[[Team:Michigan/Oil_Sands#8/26/2010|8/26/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/27/2010|8/27/2010]]
 
-
| -
 
-
|-
 
-
!Week 10
 
-
|[[Team:Michigan/Oil_Sands#8/29/2010|8/29/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/30/2010|8/30/2010]]
 
-
|[[Team:Michigan/Oil_Sands#8/31/2010|8/31/2010]]
 
-
|[[Team:Michigan/Oil_Sands#9/1/2010|9/1/2010]]
 
-
|[[Team:Michigan/Oil_Sands#9/2/2010|9/2/2010]]
 
-
|[[Team:Michigan/Oil_Sands#9/3/2010|9/3/2010]]
 
-
|[[Team:Michigan/Oil_Sands#9/4/2010|9/4/2010]]
 
-
|-
 
-
!Week 11
 
-
|[[Team:Michigan/Oil_Sands#9/5/2010|9/5/2010]]
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
|-
 
-
!Week 12
 
-
|[[Team:Michigan/Oil_Sands#9/12/2010|9/12/2010]]
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
|-
 
-
!Week 13
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
| -
 
-
|-
 
-
!Week 14
 
-
| -
 
-
| -
 
-
| -
 
-
| [[Team:Michigan/Oil_Sands#9/29/2010|9/29/2010]]
 
-
| [[Team:Michigan/Oil_Sands#9/30/2010|9/30/2010]]
 
-
| [[Team:Michigan/Oil_Sands#10/1/2010|10/1/2010]]
 
-
| -
 
-
|-
 
-
!Week 15
 
-
| [[Team:Michigan/Oil_Sands#10/3/2010|10/3/2010]]
 
-
| [[Team:Michigan/Oil_Sands#10/4/2010|10/4/2010]]
 
-
| [[Team:Michigan/Oil_Sands#10/5/2010|10/5/2010]]
 
-
| -
 
-
| [[Team:Michigan/Oil_Sands#10/7/2010|10/7/2010]]
 
-
| [[Team:Michigan/Oil_Sands#10/8/2010|10/8/2010]]
 
-
| -
 
-
|-
 
-
|}
 
-
{|cellspacing=0 style= "background: transparent"
 
-
|-valign="top"
 
-
|
 
==Oil Sands Lab Notebook==
==Oil Sands Lab Notebook==
-
This team includes [[User:annlesn|Ann Lesnefsky]], [[User:rajabiab|Bryce Rajabian]], [[User:chillywings|Marcus Lehr]], [[User:Infekt|Alex Pyden]], Jeremy Golden, John Seong Kyu Yang and [[User:kilholee|Kilho Lee]].
+
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]].
-
[[Team:Michigan/Oil_Sands_June_July]]
+
==Monthly Notebooks==
 +
Notebooks are ordered by month.
-
[[Team:Michigan/Oil_Sands_August_September]]
+
[[Team:Michigan/Oil_Sands_June_July | June/July]]
-
== Results to Date ==
+
[[Team:Michigan/Oil_Sands_August_September | August/September]]
-
[[Media:Ph7_biofilm_assay_results.xls|10/1/10 pH7 Biofilm Assay]]
+
[[Team:Michigan/Oil_Sands_October | October]]
-
[[Media:Data_10-01-10-pH7_kinetic.txt|10/1/10 pH7 Growth Curves]]
+
=='''In the Lab'''==
-
 
+
<html>
-
[[Media:Data_10-01-10-pH9_kinetic.txt|10/3/10 pH9 Growth Curves]]
+
<iframe src="http://www-personal.umich.edu/~shanwu/wiki_photos/src/themes/classic/classic-demo.html" width="100%" height="650px" scrolling="no"></iframe>
-
 
+
</html>
-
[[Media:Ph9_biofilm_assay_results.xls|10/3/10 pH9 Biofilm Assay]]
+
-
 
+
-
 
+
-
|
+
-
==='''In the Lab'''===
+
-
 
+
-
[[Image:Oilsands01.png|middle|250px]]
+
-
 
+
-
[[Image:Oilsands02.png|middle|250px]]
+
-
 
+
-
[[Image:Oilsands03.png|middle|250px]]
+
-
 
+
-
[[Image:Oilsands07.png|middle|250px]]
+
-
 
+
-
[[Image:Oilsands04.png|middle|250px]]
+
-
 
+
-
[[Image:Oilsands06.png|middle|250px]]
+
-
 
+
-
[[Image:Oilsands05.png|middle|250px]]
+
-
 
+
-
|}
+
-
 
+
-
==10/1/2010==
+
-
''Alex''
+
-
 
+
-
Moved broth cultures 37°C to 4°C -- 1:30pm (19-hr culture)
+
-
Prepared biofilm assay plate for all pH9 tests - following [[Media:Static+biofilm+quantification.pdf|Alex's biofilm assay protocol]]
+
-
*plate template:
+
-
[[image:9-30 plate template.jpg]]
+
-
**100 μL/well: 99 μL medium + 1 μL culture
+
-
*stored plate in Lin Lab 4°C -- 2:20pm
+
-
----
+
-
Saved data for curves from ph7 plate
+
-
Read pH7 plate ODs
+
-
Performed biofilm assay on ph7 plate
+
-
Started 24-hr kinetic reading for pH9 plate -- ~midnight
+
-
 
+
-
Discarded pH7 plate
+
-
 
+
-
Processed pH7 plate data
+
-
*uploaded results [[Media:Ph7_biofilm_assay_results.xls|here]]
+
-
Uploaded pH7 kinetic data [[Media:Data_10-01-10-pH7_kinetic.txt|here]]
+
-
 
+
-
== 10/3/10 ==
+
-
''Alex''
+
-
 
+
-
Ran CV biofilm assay on pH9 plate, following [[Media:Static+biofilm+quantification.pdf‎|my protocol]]
+
-
*discarded plate
+
-
*uploaded [[Media:Ph9_biofilm_assay_results.xls|results]]
+
-
*uploaded [[Media:Data_10-01-10-pH9_kinetic.txt|pH9 kinetic raw data]]
+
-
 
+
-
== 10/4/2010 ==
+
-
''Marcus and Ben''
+
-
 
+
-
Performed ligation of Flu operon and pSB1AT3 according to the Ginko Bioworks [[Media:Ligation_Protocol.pdf|Ligation]] protocol, with modifications.
+
-
 
+
-
*Calculated amount from digests to add to ligation for 1:1 and 3:1 insert:vector ratios
+
-
**Amount of DNA in digests:
+
-
***Flu PCR- 29.8 ng/uL x 17 uL= 506.6 ng / 50 uL = 10.132 ng/uL
+
-
***pSB1AT3- 240.5 ng/uL x 5 uL= 1202.5 ng / 50 uL = 24.05 ng/uL
+
-
**Used an online calculator to find moles:
+
-
***Flu PCR- 230.81 fmol/50 uL
+
-
***pSB1AT3- 537.68 fmol/50 uL
+
-
***This gives a molar ratio of 0.4293
+
-
 
+
-
1:1 Ligation Mix
+
-
*4 uL Flu PCR x 10.132 ng/uL= 40.528 ng
+
-
*1.7 uL pSB1AT3 x 24.05 ng/uL= 40.885 ng
+
-
*2 uL T4 Buffer
+
-
*1 uL T4 Ligase
+
-
*11.3 uL Ultra pure H2O
+
-
 
+
-
3:1 Ligation Mix
+
-
*2 uL Flu PCR x 10.132 ng/uL= 20.264 ng
+
-
*2.57 uL pSB1AT3 x 24.05 ng/uL= 61.809 ng
+
-
*2 uL T4 Buffer
+
-
*1 uL T4 Ligase
+
-
*12.43 uL Ultra pure H2O
+
-
 
+
-
Note that the conversion factor for the 3:1 ligation mixture was applied in reverse, and thus it was actually a 1:3 insert:vector ratio.
+
-
 
+
-
Ligation program was the same as used in the [[Media:Ligation_Protocol.pdf|Ligation]] protocol.
+
-
 
+
-
== 10/5/2010 ==
+
-
''Marcus''
+
-
 
+
-
Performed transformation according to [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC145660/pdf/240536.pdf Pope & Kent (1996)].
+
-
 
+
-
Transformed Parts
+
-
*Flu/pSB1AT3 1:1 ligation
+
-
*Flu/pSB1AT3 1:3 ligation
+
-
*VP130
+
-
*J61100
+
-
*OmpA
+
-
*Cell only negative control
+
-
 
+
-
Procedure
+
-
*2 uL of DNA was pipetted into PCR tube on ice and transferred to Lin lab
+
-
*Comp cells were thawed on ice and 50 uL was pipetted into each tube with a chilled pipette on ice
+
-
**Cells were pipetted up and down to mix throughly
+
-
*Cells were kept on ice and brought back to ERB
+
-
*Cells were plated directly onto pre-warmed plates with appropriate antibiotics
+
-
**Kevin put plates in incubator several hours before hand
+
-
 
+
-
It should be noted that two 200 uL aliquots of cells had to be thawed, and one was labeled "Thawed" and returned to the -80 C. Thawing should be avoided if possible.
+
-
 
+
-
Also, made two 5 mL LD1/LD2 co-cultures in M9+Sigma and Acros NAs, pH 7 and pH 9. Also made 2 mL pure cultures at pH 7. All culture tubes were stored in the 30 C. These cultures were made to assay growth, make new stock plates, and determine if colony morphology can be used to distinguish between species in a co-culture.
+
-
 
+
-
== 10/7/2010 ==
+
-
''Marcus''
+
-
 
+
-
Ben moved transformation plates to 4 C yesterday, control plates were blank, and all plates except for J61100 appeared to have colonies. The Flu/pSB1AT3 ligation plates had very small colonies, so they were returned to the incubator with the J61100 plate. Also, it could be seen that many colonies on the 1:3 ligation plate appeared red, indicating that the vector had preferentially reformed. This could be because of the ratio, but dephosphorylation treatment should be used in the future for ligations.
+
-
 
+
-
OD600's were taken of the Pseudomonas cultures (46 hours)
+
-
*Putida pH 7- 0.157
+
-
*Fluorescens pH 7- 0.129
+
-
*Co-culture pH 7- 0.188
+
-
*Co-culture pH 9- 0.232
+
-
 
+
-
Surprisingly, they seem to grow better at pH 9, at least in co-culture. As expected, the co-culture did better than pure cultures. This lends some support towards Alex's biofilm assay results, however, it should still be repeated. Also, plated a serial dilution of the pH 9 co-culture, at 10<sup>-5</sup>, 10<sup>-6</sup>, and 10<sup>-7</sup> dilutions to determine the conversion factor between OD600 and cell count. Made streak plates of all other cultures, pure cultures for stock, and pH 7 co-culture to determine if colonies could be distinguished. All cultures and plates were returned to the 30<sup>o</sup>C incubator, without shaking.
+
-
 
+
-
== 10/8/2010 ==
+
-
''Marcus''
+
-
 
+
-
Kevin removed the transformation plates which were placed back in the incubator to the 4<sup>o</sup>C around 1 pm.
+
-
 
+
-
The [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC145660/pdf/240536.pdf Pope & Kent (1996)] appears to be very efficient, as the plates were full of colonies:
+
-
 
+
-
[[Image:5 Transformation Plates.jpg|thumb|500px]]
+
-
 
+
-
Next time suspending the cells in water before spreading, or even making dilutions should be tried.
+
-
 
+
-
PCR Screening:
+
-
8 colonies were picked from each transformation plate except for VP130, and suspended in 50 uL of water on a microplate.
+
-
 
+
-
*Plate Layout
+
-
**Row 1- Flu 1:1
+
-
**Row 2- Flu 1:3
+
-
**Row 3- OmpA
+
-
**Row 4- J61100
+
-
 
+
-
The first two rows (Flu 1:1 and 1:3) were PCR'd by adding 1 uL of each sample to a PCR tube with a drop of mineral oil in them. A master mix was made, and 50 uL was added to each tube (should have been 49 uL).
+
-
 
+
-
Master Mix (18x)
+
-
*180 uL 5x Phusion Buffer
+
-
*18 uL 10 mM dNTPs
+
-
*45 uL VF2
+
-
*45 uL VR
+
-
*9 uL Phusion polymerase
+
-
*585 uL Ultra pure H2O
+
-
 
+
-
PCR Program
+
-
*1. 95 C for 10 min
+
-
*2. 95 C for 30 sec
+
-
*3. 62 C for 30 sec
+
-
*4. 72 C for 2 min
+
-
*5. Return to step two 34 times
+
-
*6. 72 C for 10 min
+
-
*7. 4 C store
+
-
 
+
-
This PCR protocol was constructed from the following sources:
+
-
*[http://openwetware.org/wiki/Engineering_BioBrick_vectors_from_BioBrick_parts/Colony_PCR_protocol OpenWetWare BioBrick Primers Colony PCR]
+
-
*[http://openwetware.org/wiki/Endy:Colony_PCR OpenWetWare Endy Colony PCR]
+
-
*[http://www.finnzymes.com/pdf/f530sl_phusion_datasheet_2_2_low.pdf Finnzymes Phusion Manual]
+
-
 
+
-
Also- loosened the lids on Pseudomonas liquid cultures to provide air exchange, and returned yesterday's Pseduomonas plates to 30C incubator, without shaking.
+
-
 
+
-
== 10/16/2010 ==
+
-
''Nick''
+
-
 
+
-
10-16-10 Psuedomonas Competent Cell Preparation
+
-
 
+
-
[[Media:Quick Transformation of E. coli Competant Cell Preperation.pdf| Protocol - Competent Cell Preparation for Quick Transformation of E. coli]]
+
-
 
+
-
Ben Parker started the overnight cultures and assisted in OD measurement and initial centrifugation steps.
+
-
 
+
-
A colony of P. putida and P. fluorescence was picked from LB agar plates (10/6/10) and grown up in an overnight culture in 2ml Amp at 30 C.
+
-
 
+
-
The overnight culture was added to 100 ml of LB media and grown at 30C for 4 hours.
+
-
 
+
-
Protocol was carried out approximately 20 minutes after the following OD600 was recorded:
+
-
+
-
Blank - water
+
-
 
+
-
P. putida – 0.587
+
-
 
+
-
P. Fluorescence – 0.610
+
-
 
+
-
One centrifuge tube containing p. putida culture failed during centrifugation at 5000 rpm. The protocol was altered by reducing the speed to 2500 rpm after this point to reduce the chance of failure. The cells are stored in the 4C fridge in room 1239.
+

Latest revision as of 00:05, 27 October 2010


Michigan Header





Oil Sands Lab Notebook

Members of this team include Ann Lesnefsky, Bryce Rajabian, Marcus Lehr, Alex Pyden, Jeremy Golden, John Seong Kyu Yang and Kilho Lee.

Monthly Notebooks

Notebooks are ordered by month.

June/July

August/September

October

In the Lab

Retrieved from "http://2010.igem.org/Team:Michigan/Oil_Sands"