Team:Alberta/Notebook/CreatingParts

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{{Team:Alberta/beginMainContent}}
{{Team:Alberta/beginMainContent}}
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=Creating Parts=
+
=Creating Parts and Testing Experiments=
 +
===Project Timeline: Click on an image to see more information===
 +
<html>
 +
<img src="https://static.igem.org/mediawiki/2010/b/b2/CreatingPartsTimeline.jpg" border="0" usemap="#CreatingParts">
 +
<map name="CreatingParts">
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<area shape="rect" coords="0, 0, 102, 62" href="https://2010.igem.org/wiki/index.php?title=Team:Alberta/Notebook/CreatingParts#PCRing_Antibiotic_Resistance_Markers">
 +
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<area shape="rect" coords="125, 0, 267, 58" href="https://2010.igem.org/wiki/index.php?title=Team:Alberta/Notebook/CreatingParts#The_Wintergreen_Experiment_and_the_Photobacterial_Construct">
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<area shape="rect" coords="222, 70, 319, 121" href="https://2010.igem.org/wiki/index.php?title=Team:Alberta/Notebook/CreatingParts#AB_chlor_and_tet_parts">
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-----
==PCRing Antibiotic Resistance Markers==
==PCRing Antibiotic Resistance Markers==
*May 25, 2010  
*May 25, 2010  
:PCRed the antibiotic resistance marker biobytes (Ampicillin, Tetracycline and Chlormaphenicol) that are analogous to the kanamycin PCR fragements.  
:PCRed the antibiotic resistance marker biobytes (Ampicillin, Tetracycline and Chlormaphenicol) that are analogous to the kanamycin PCR fragements.  
-
::Ampicillin: Primers = Pr.A.SB4A5.Apr+ and Pr.B. SB4A5.Apr -  
+
::*Ampicillin:
-
Template = pSB4A5
+
:::Primers = Pr.A.SB4A5.Apr+ and Pr.B. SB4A5.Apr -  
-
::Chloramphenical: Primers = Pr. A. SB4C5.Chr + and Pr.B.SB4A5.Chr -
+
:::Template = pSB4A5
-
Template = pSB4C5
+
::*Chloramphenical:
-
::Tetracycline: Primers = Pr.A.SB3T5.Tr+ and Pr.B.PSB3T5.Tr -
+
:::Primers = Pr. A. SB4C5.Chr + and Pr.B.SB4A5.Chr -
-
Template = pSB3T5
+
:::Template = pSB4C5
 +
::*Tetracycline:
 +
:::Primers = Pr.A.SB3T5.Tr+ and Pr.B.PSB3T5.Tr -
 +
:::Template = pSB3T5
-
==Ampillicin Resistance AB in pSB1C3==
+
==AB Ampillicin Resistance gene in pSB1C3==
-
*June 3, 2010: PCR Ampillicin  Resistance (AmpR) AB BioByte.
+
*June 3, 2010:
-
*June 9, 2010: Digested AmpR AB with BsaI.
+
:PCR Ampillicin  Resistance (AmpR) AB BioByte.
-
*June 10, 2010: Digested pSB1C3 Vector with BsaHF.
+
*June 9, 2010:
-
Ligated and transformed AmpR AB with pSB1C3 Vector.
+
:Digested AmpR AB with BsaI.
-
*June 17, 2010: Miniprepped AmpR + pSB1C3.
+
*June 10, 2010:
 +
:Digested pSB1C3 Vector with BsaHF.
 +
:Ligated and transformed AmpR AB with pSB1C3 Vector.
 +
*June 17, 2010:
 +
:Miniprepped AmpR + pSB1C3.
 +
 
 +
==The Wintergreen Experiment and the Photobacterial Construct==
 +
 
 +
===L'Oreal Wintergreen Experiment:===
 +
We tried to see if the salicyclic acid in a cosmetic product could be used as a substrate for the wintergreen smell device.
 +
 
 +
:*June 11, 2010 - Preparation of plates
 +
:*June 12, 2010 - Testing of growth
 +
 
 +
===Testing of the photobacterial construct:===
 +
We tried to see if the photobacterial construct could be created using without using X-gal cleavage as a basis for visualization of the colonies.
 +
 
 +
:*June 28, 2010 - Preparation of biobricks
 +
:*July 22, 2010 - Creation of promoter and inducer parts
 +
:*July 26, 2010 - Final biobrick assembly
 +
:*July 28, 2010 - Creation of system with carotenoid marker
 +
:*August 5, 2010 - Complete preparation with light during growth
==AB chlor and tet parts==
==AB chlor and tet parts==
-
Strategy: digest both AB kan PCR product and pSB1A3 with NotI, and ligate. Then, cut chlor and tet AB PCR products with BsaI and cut out the kan from the plasmid using BsaI, and ligate chlor or tet into it.
+
===Strategy:===
 +
:Digest both AB kan PCR product and pSB1A3 with NotI, and ligate. Then, cut chlor and tet AB PCR products with BsaI and cut out the kan from the plasmid using BsaI, and ligate chlor or tet into it.
 +
 
 +
*June 30, 2010:
 +
:Digested PCR product kan AB and pSB1A3 with NotI. Ligated the kan and pSB1A3 together.
 +
*July 5, 2010:
 +
:Transformed from the ligation of kan and pSB1A3.
 +
*July 6, 2010:
 +
:White colonies. Set up overnights.
 +
*July 7, 2010:
 +
:Made minipreps from the overnights and digested them with XbaI and PstI to check for proper orientation.  Digested those in correct orientation with BsaI to remove kan. Digested PCR product chlor AB and tet AB with BsaI. Ligated chlor and tet separately with the PSB1A3 backbone.
 +
*July 8, 2010:
 +
:Transformed from ligations of chlor and tet AB with pSB1A3 backbone.
 +
*July 9, 2010:
 +
:White colonies. Set up overnights.
 +
*July 10, 2010:
 +
:Minipreps were done and were digested with EcoRI to test for size.
 +
*July 13, 2010:
 +
:Digested kan, tet and amp AB’s with BsaIHF.
 +
*July 14, 2010:
 +
:Digested kan, chlor, tet and amp AB’s with XbaI and PstI.
 +
*July 20, 2010:
 +
:Glycerol stocks were made of chlor and tet AB.
 +
*August 9, 2010:
 +
:Sequenced AB amp (tube A) (from Anh’s previous work), tet (tube B1) and chlor (tube D1). All look good.
 +
*August 13, 2010:
 +
:Transformed from the successful, sequenced tubes.
 +
*August 16-17, 2010:
 +
:White colonies. Made maxipreps, after inoculation from transformed plates, of AB chlor (pC.s.A.005) and amp (pC.s.A.003)
 +
*August 18, 2010:
 +
:Digested the maxipreps with BsaI.
 +
==Production of BioByte Parts:==
 +
Parts are created by PCR, digested with BsaI, and put into the parts plasmids as demonstrated by mWasabi.
 +
:*Aug 12,2010 PCR amplification of CrtE,CrtB,CrtI, CrtY, CrtZ, VioA, VioB, VioC, VioD, VioE, araC, lacI, tetR, CI
 +
:**Amplification failed
 +
:*Aug 13,2010  Troubleshoot amplification and PCR CrtY with primers leaving a BsaI cut site leaving characteristic A BioByte Overhangs
 +
:*Aug 14, 2010 PCR CrtB, CrtE, CrtY, VioA, vioD vioE, AraC, lacI parts with primers leaving a BsaI cut site leaving characteristic A BioByte Overhangs
 +
:*Aug 16, 2010 Digested all parts and BsaI Base Plasmids with BsaI, ligated together and transformed.
 +
:*Aug 17, 2010 There were red and white colonies of all parts. 
 +
:*Aug 18, 2010 Digested Minipreps of colonies and expected band lengths were observed. 
-
June 30, 2010 Digested PCR product kan AB and pSB1A3 with NotI. Ligated the kan and pSB1A3 together. Gel “29.06.10.alina 2”
+
===Parts were sequenced to confirm expected sequences:===
-
July 5, 2010 Transformed from the ligation of kan and pSB1A3.
+
:*Sept. 9-Oct. 9, 2010. Made and confirmed sequences of eCFP and mRFP parts.
-
July 6, 2010 White colonies. Set up overnights.
+
-
July 7, 2010 Made minipreps from the overnights and digested them with XbaI and PstI to check for proper orientation. Gel “07.07.10.alina”? Digested those in correct orientation with BsaI to remove kan. Digested PCR product chlor AB and tet AB with BsaI. Ligated chlor and tet separately with the PSB1A3 backbone. Gel “07.07.10.karinaalina2”?
+
-
July 8, 2010 Transformed from ligations of chlor and tet AB with pSB1A3 backbone.
+
-
July 9, 2010 White colonies. Set up overnights.
+
-
July 10, 2010 Minipreps were done and were digested with EcoRI to test for size. Gel “07.10.10.alina”?
+
-
July 13, 2010 Digested kan, tet and amp AB’s with BsaIHF. Gel “13.07.10.alina2”
+
-
July 14, 2010 Digested kan, chlor, tet and amp AB’s with XbaI and PstI. Gel “14.07.10.alina” **********ARE THESE Bfu ones? Probably not.
+
-
July 20, 2010 Glycerol stocks were made of chlor and tet AB.
+
-
August 9, 2010 Sequenced AB amp (tube A) (from Anh’s previous work), tet (tube B1) and chlor (tube D1). All look good.
+
-
August 13, 2010 Transformed from the successful, sequenced tubes.
+
-
August 16-17, 2010 White colonies. Made maxipreps, after inoculation from transformed plates, of AB chlor (pC.s.A.005) and amp (pC.s.A.003)
+
-
August 18, 2010 Digested the maxipreps with BsaI. Gel “18.08.10.alina”
+
-
==Bsa BA amp and tet==
+
==BA amp and tet Parts==
-
August 19, 2010 Performed PCR using AB amp in pSB1C3, AB chlor in pSB1A3, and AB tet in pSB1A3 as templates to obtain BA amp, tet, chlor products.  
+
*August 19, 2010:
-
August 20, 2010 Gel “20.08.10.aina”. Digested BA amp and tet products and BA pSB1C3 backbone with BsaI. Ligated. Transformed. Gel “20.08.10.alina2” (bad gel)
+
:Performed PCR using AB amp in pSB1C3, AB chlor in pSB1A3, and AB tet in pSB1A3 as templates to obtain BA amp, tet, chlor products.  
-
August 21, 2010 5 white colonies on tet, lot of colonies on amp.
+
*August 20, 2010:
-
August 22, 2010 Set up overnights from colonies.
+
: Digested BA amp and tet products and BA pSB1C3 backbone with BsaI. Ligated. Transformed.  
-
August 23, 2010 Miniprepped BA amp and chlor.  
+
*August 21, 2010:
-
August 24, 2010 Digested BA amp and chlor with BsaI gel “24.08.10.alina”
+
:5 white colonies on tet, lot of colonies on amp.
-
August 25, 2010 Digested BA amp and chlor with EcoRI gel “25.08.10.alina*”,  XbaI and PstI “25.08.10.alina2”
+
*August 22, 2010:
-
August 26, 2010 Sequenced BA amp. ***Resequenced on September 7th - Looks good. Transformed AB tet on [1/4 tet].
+
:Set up overnights from colonies.
-
August 27, 2010 White colonies, streaked on [1/2 tet]
+
*August 23, 2010:
-
August 28, 2010 White streaks with individual colonies. Set up overnights of AB tet.  
+
:Miniprepped BA amp and chlor.  
-
August 31, 2010 Minipreps of AB tet. Digested them with BsaI. Great gel “31.08.10 Alina”
+
*August 24, 2010:
-
September 1, 2010 Performed PCR (like Aug 19) using AB amp in pSB1C3, AB chlor in pSB1A3, and AB tet in pSB1A3 as templates. One tube was from sequenced tet and one from the re-transformed sequenced tet. Gel “01.09.10.alina”. Digest PCR products and BA kan in pSB1C3 with BsaI. LIgated. Transformed.
+
:Digested BA amp and chlor with BsaI
-
September 6, 2010 White colonies. Set up overnights of tet BA.
+
*August 25, 2010:
-
September 7, 2010 Miniprepped the overnights of tet Ba.  
+
:Digested BA amp and chlor with EcoRI,  XbaI and PstI  
-
September 13, 2010 Digested tet BA with BsaI gel “13.09.10.alina*”
+
*August 26, 2010:
-
September 15, 2010 Sequenced tet BA. Looks good.
+
:Sequenced BA amp. ***Resequenced on September 7th - Looks good. Transformed AB tet on [1/4 tet].
 +
*August 27, 2010:
 +
:White colonies, streaked on [1/2 tet]
 +
*August 28, 2010:
 +
:White streaks with individual colonies. Set up overnights of AB tet.  
 +
*August 31, 2010:
 +
:Minipreps of AB tet. Digested them with BsaI.
 +
*September 1, 2010:
 +
:Performed PCR (like Aug 19) using AB amp in pSB1C3, AB chlor in pSB1A3, and AB tet in pSB1A3 as templates. One tube was from sequenced tet and one from the re-transformed sequenced tet. Digest PCR products and BA kan in pSB1C3 with BsaI. Ligated. Transformed.
 +
*September 6, 2010:
 +
:White colonies. Set up overnights of tet BA.
 +
*September 7, 2010:
 +
:Miniprepped the overnights of tet Ba.  
 +
*September 13, 2010:
 +
:Digested tet BA with BsaI  
 +
*September 15, 2010:
 +
:Sequenced tet BA. Looks good.
==Chlor BA==
==Chlor BA==
First, we have to make a Bsa BA pSB1A3 backbone by digesting pSB1A3 with XbaI and PstI and inserting Bsa BA kan. Then, the kan is cut out with BsaI and chlor BA is placed in.
First, we have to make a Bsa BA pSB1A3 backbone by digesting pSB1A3 with XbaI and PstI and inserting Bsa BA kan. Then, the kan is cut out with BsaI and chlor BA is placed in.
-
September 17, 2010 Digested pSB1A3 and BA kan with XbaI and PstI gel “17.09.10.alina”. Ligated. Transformed.
+
*September 17, 2010:
-
September 18, 2010 White colonies. Set up overnights of BA kan in pSB1A3 backbone.
+
:Digested pSB1A3 and BA kan with XbaI and PstI. Ligated. Transformed.
-
September 20, 2010 Miniprepped overnights of BA kan in pSB1A3 backbone.
+
*September 18, 2010:
-
September 24, 2010 Digested the BA kan in pSB1A3 backbone and BA chlor PCR product (from Sept. 1) with BsaI. Ligated.  
+
:White colonies. Set up overnights of BA kan in pSB1A3 backbone.
-
September 27, 2010 Transformed.
+
*September 20, 2010:
-
September 29, 2010 White colonies. Set up overnights.
+
:Miniprepped overnights of BA kan in pSB1A3 backbone.
-
September 30, 2010 Made minipreps of BA chlor.
+
*September 24, 2010:
-
October 1, 2010 White Colonies. Digested BA chlor in pSB1A3 backbone with BsaI gel “08.10.10.alina”
+
:Digested the BA kan in pSB1A3 backbone and BA chlor PCR product (from Sept. 1) with BsaI. Ligated.  
 +
*September 27, 2010:
 +
:Transformed.
 +
*September 29, 2010:
 +
:White colonies. Set up overnights.
 +
*September 30, 2010:
 +
:Made minipreps of BA chlor.
 +
*October 1, 2010:
 +
:White Colonies. Digested BA chlor in pSB1A3 backbone with BsaI  
{{Team:Alberta/endMainContent}}
{{Team:Alberta/endMainContent}}

Latest revision as of 10:51, 27 October 2010

TEAM ALBERTA

Creating Parts and Testing Experiments

Project Timeline: Click on an image to see more information

PCRing Antibiotic Resistance Markers

  • May 25, 2010
PCRed the antibiotic resistance marker biobytes (Ampicillin, Tetracycline and Chlormaphenicol) that are analogous to the kanamycin PCR fragements.
  • Ampicillin:
Primers = Pr.A.SB4A5.Apr+ and Pr.B. SB4A5.Apr -
Template = pSB4A5
  • Chloramphenical:
Primers = Pr. A. SB4C5.Chr + and Pr.B.SB4A5.Chr -
Template = pSB4C5
  • Tetracycline:
Primers = Pr.A.SB3T5.Tr+ and Pr.B.PSB3T5.Tr -
Template = pSB3T5

AB Ampillicin Resistance gene in pSB1C3

  • June 3, 2010:
PCR Ampillicin Resistance (AmpR) AB BioByte.
  • June 9, 2010:
Digested AmpR AB with BsaI.
  • June 10, 2010:
Digested pSB1C3 Vector with BsaHF.
Ligated and transformed AmpR AB with pSB1C3 Vector.
  • June 17, 2010:
Miniprepped AmpR + pSB1C3.

The Wintergreen Experiment and the Photobacterial Construct

L'Oreal Wintergreen Experiment:

We tried to see if the salicyclic acid in a cosmetic product could be used as a substrate for the wintergreen smell device.

  • June 11, 2010 - Preparation of plates
  • June 12, 2010 - Testing of growth

Testing of the photobacterial construct:

We tried to see if the photobacterial construct could be created using without using X-gal cleavage as a basis for visualization of the colonies.

  • June 28, 2010 - Preparation of biobricks
  • July 22, 2010 - Creation of promoter and inducer parts
  • July 26, 2010 - Final biobrick assembly
  • July 28, 2010 - Creation of system with carotenoid marker
  • August 5, 2010 - Complete preparation with light during growth

AB chlor and tet parts

Strategy:

Digest both AB kan PCR product and pSB1A3 with NotI, and ligate. Then, cut chlor and tet AB PCR products with BsaI and cut out the kan from the plasmid using BsaI, and ligate chlor or tet into it.
  • June 30, 2010:
Digested PCR product kan AB and pSB1A3 with NotI. Ligated the kan and pSB1A3 together.
  • July 5, 2010:
Transformed from the ligation of kan and pSB1A3.
  • July 6, 2010:
White colonies. Set up overnights.
  • July 7, 2010:
Made minipreps from the overnights and digested them with XbaI and PstI to check for proper orientation. Digested those in correct orientation with BsaI to remove kan. Digested PCR product chlor AB and tet AB with BsaI. Ligated chlor and tet separately with the PSB1A3 backbone.
  • July 8, 2010:
Transformed from ligations of chlor and tet AB with pSB1A3 backbone.
  • July 9, 2010:
White colonies. Set up overnights.
  • July 10, 2010:
Minipreps were done and were digested with EcoRI to test for size.
  • July 13, 2010:
Digested kan, tet and amp AB’s with BsaIHF.
  • July 14, 2010:
Digested kan, chlor, tet and amp AB’s with XbaI and PstI.
  • July 20, 2010:
Glycerol stocks were made of chlor and tet AB.
  • August 9, 2010:
Sequenced AB amp (tube A) (from Anh’s previous work), tet (tube B1) and chlor (tube D1). All look good.
  • August 13, 2010:
Transformed from the successful, sequenced tubes.
  • August 16-17, 2010:
White colonies. Made maxipreps, after inoculation from transformed plates, of AB chlor (pC.s.A.005) and amp (pC.s.A.003)
  • August 18, 2010:
Digested the maxipreps with BsaI.

Production of BioByte Parts:

Parts are created by PCR, digested with BsaI, and put into the parts plasmids as demonstrated by mWasabi.

  • Aug 12,2010 PCR amplification of CrtE,CrtB,CrtI, CrtY, CrtZ, VioA, VioB, VioC, VioD, VioE, araC, lacI, tetR, CI
    • Amplification failed
  • Aug 13,2010 Troubleshoot amplification and PCR CrtY with primers leaving a BsaI cut site leaving characteristic A BioByte Overhangs
  • Aug 14, 2010 PCR CrtB, CrtE, CrtY, VioA, vioD vioE, AraC, lacI parts with primers leaving a BsaI cut site leaving characteristic A BioByte Overhangs
  • Aug 16, 2010 Digested all parts and BsaI Base Plasmids with BsaI, ligated together and transformed.
  • Aug 17, 2010 There were red and white colonies of all parts.
  • Aug 18, 2010 Digested Minipreps of colonies and expected band lengths were observed.

Parts were sequenced to confirm expected sequences:

  • Sept. 9-Oct. 9, 2010. Made and confirmed sequences of eCFP and mRFP parts.

BA amp and tet Parts

  • August 19, 2010:
Performed PCR using AB amp in pSB1C3, AB chlor in pSB1A3, and AB tet in pSB1A3 as templates to obtain BA amp, tet, chlor products.
  • August 20, 2010:
Digested BA amp and tet products and BA pSB1C3 backbone with BsaI. Ligated. Transformed.
  • August 21, 2010:
5 white colonies on tet, lot of colonies on amp.
  • August 22, 2010:
Set up overnights from colonies.
  • August 23, 2010:
Miniprepped BA amp and chlor.
  • August 24, 2010:
Digested BA amp and chlor with BsaI
  • August 25, 2010:
Digested BA amp and chlor with EcoRI, XbaI and PstI
  • August 26, 2010:
Sequenced BA amp. ***Resequenced on September 7th - Looks good. Transformed AB tet on [1/4 tet].
  • August 27, 2010:
White colonies, streaked on [1/2 tet]
  • August 28, 2010:
White streaks with individual colonies. Set up overnights of AB tet.
  • August 31, 2010:
Minipreps of AB tet. Digested them with BsaI.
  • September 1, 2010:
Performed PCR (like Aug 19) using AB amp in pSB1C3, AB chlor in pSB1A3, and AB tet in pSB1A3 as templates. One tube was from sequenced tet and one from the re-transformed sequenced tet. Digest PCR products and BA kan in pSB1C3 with BsaI. Ligated. Transformed.
  • September 6, 2010:
White colonies. Set up overnights of tet BA.
  • September 7, 2010:
Miniprepped the overnights of tet Ba.
  • September 13, 2010:
Digested tet BA with BsaI
  • September 15, 2010:
Sequenced tet BA. Looks good.

Chlor BA

First, we have to make a Bsa BA pSB1A3 backbone by digesting pSB1A3 with XbaI and PstI and inserting Bsa BA kan. Then, the kan is cut out with BsaI and chlor BA is placed in.

  • September 17, 2010:
Digested pSB1A3 and BA kan with XbaI and PstI. Ligated. Transformed.
  • September 18, 2010:
White colonies. Set up overnights of BA kan in pSB1A3 backbone.
  • September 20, 2010:
Miniprepped overnights of BA kan in pSB1A3 backbone.
  • September 24, 2010:
Digested the BA kan in pSB1A3 backbone and BA chlor PCR product (from Sept. 1) with BsaI. Ligated.
  • September 27, 2010:
Transformed.
  • September 29, 2010:
White colonies. Set up overnights.
  • September 30, 2010:
Made minipreps of BA chlor.
  • October 1, 2010:
White Colonies. Digested BA chlor in pSB1A3 backbone with BsaI


Retrieved from "http://2010.igem.org/Team:Alberta/Notebook/CreatingParts"