Team:Macquarie Australia/Notebook

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Revision as of 02:17, 12 September 2013

Notebook

To browse through our notebook simply click on the image with the date. It will expand with what we did that week. To continue on simply click on the next one. If the notebook isn't functioning as planned (it will not load the next tab of content) then please go to our linearised view which is located here.

A seperate 'Results & Characterization' section has been created to show and highlight our successful accomplishments, shown Here.

Intro to the week, Work being done, "Using PCR we amplified the genes X and X"
Results (This worked, this didnt), "Gene X didnt amplify, Gene X did"
Small discussion + Whats next "We plan on then doing X to amplified gene"

Month 1 - Summer Break

We spent this week designing the sequences of the genes: ChlI1, CTH1, CHlM, POR, CHlD, ChlH, GUN4 and Plastocyanin that we will use for the project, including gBlocks and PCR products. The gBlocks were designed to eliminate unwanted restriction endonuclease sites, encode restriction enzyme sites EcoR1 (E), Xbal (X), SpeI (S) and PstI (P) at the ends of the gBlocks and possess 35bp overlaps between the gBlocks and PCR products that comprise each gene separately. Each gene sequence was ensured to have a bacterial ribosome binding site (shine-dalgarno sequence).

gBLocks:
1. ChlI1 - 1 gBlock + 2 PCR products
2. ChlH - 5 gBlocks + 3 PCR products
3. ChlD - 1 gBlock + 2 PCR products
4. GUN4 - 1 gBlock + 1 PCR product
5. ChlM - 1 gBlock + 1 PCR product
6. CTH1 - 2 gBlocks + 1 PCR products
7. POR - 1 gBlock + 1 PCR product
8. Plastocyanin - 1 gBlock

Short and long primers for the PCR products were designed. Long primers (only reverse primers) included restriction sites S and P, however the short primers were both forward and reverse primers.

included restriction sites S and P, however the short primers were both forward and reverse primers.

Primers:
GUN4-F1 AAGCGCAACTGGGTTTACTTC
GUN4-R1S ATACAACACCTGGCAGGATCA
GUN4-R1L CAGCGGCGGCCTACTAGTATACAACACCTGGCAGG
ChlM-F1 AGACGGTGGACAAGGTGCT
CHLM-R1S GTCCGAGTCCATCAGTCCTTAC
CHLM-R1L CAGCGGCCGCCTACTAGTCCGAGTCCATCAGTCC
ChlD-F1 CCCGTGGAAGACCAAGATGC
ChlD-R1S GTAACGCTCACATACCAACAC
ChlD-R1L CAGCGGCCGCCTACTAGTAACGCTCACATACCAAC
Chll1-F1 AGCTGATGAGCGAGGAGGT
Chll1-R1S TGCCGCTTACTCCATGCCG
Chll1-R1L CAGCGGCCGCCTACTAGTGCCGCTGACTCCATG
CTH1-F1 CGGAGATGGTCAACGACTG
CTH-R1S GCTCCAAAGCACTCTCAAAACT
CTHR1L CAGCGGCCGCCTACTAGTGCTCCAAAGCACTCTC
ChlH-F1 GCTCATCTTCATTGAGGAGCTT
ChlH-R1 GCTGTTCACGAAGTTCTTG
ChlH-F2 GAGGATCTGATCCAGTCGGT
ChlH-R2 CTGGTCAACGTCAGCCAGGA
ChlH-F3 GAGATGTACCTGAAGCGCAAG
ChlH-R3S ACTAGTGCTACCATGAAGGG
ChlH-R3L CAGCGGCCGCCTACTAGTGCTACCATGAAGGG
POR-F1 ACTCAATCCTGCACCTGGAC
POR-R1S CAGAGACGAACCGCAGGTAG
POR-R1L CAGCGGCCGCCTACTAGTCAGAGACGAACCGCAG

Week 1 - Thursday August 1st

With the break between semesters over, the Macquarie iGEM team returned to classes; for many of us this was the first day of iGEM 2013. We had our first meeting and discussed our project. Dr. Louise Brown and Associate Professor Rob Willows were introduced to the team and we began to determine who would take on certain roles within the team.

We eagerly began our project, deciding to use Gibson Assembly to produce our optimised genes. We had decided to develop BioBricks necessary for the biosynthesis of chlorophyll within E.coli. To do this, we constructed a gene pathway, containing 12 genes to reach our goal of chlorophyll biosynthesis.

Week 2 - Thursday August 8th

Week 2 (G block assemblies & transformations) - Update Coming soon

Retrieved from "http://2013.igem.org/Team:Macquarie_Australia/Notebook"

@@ Line 106: / Line 106: @@
 <p>We spent this week designing the sequences of the genes: ChlI1, CTH1, CHlM, POR, CHlD, ChlH, GUN4 and Plastocyanin that we will use for the project, including gBlocks and PCR products. The gBlocks were designed to eliminate unwanted restriction endonuclease sites, encode restriction enzyme sites EcoR1 (E), Xbal (X), SpeI (S) and PstI (P) at the ends of the gBlocks and possess 35bp overlaps between the gBlocks and PCR products that comprise each gene separately. Each gene sequence was ensured to have a bacterial ribosome binding site (shine-dalgarno sequence).</p>
+<b>gBLocks:</b><br>
 . ChlI1                   - 1 gBlock + 2 PCR products<br>
 . ChlH                   - 5 gBlocks + 3 PCR products<br>
@@ Line 114: / Line 115: @@
 .  POR                      - 1 gBlock + 1 PCR product<br>
 .  Plastocyanin       - 1 gBlock<br>
+<p>Short and long primers for the PCR products were designed. Long primers (only reverse primers) included restriction sites S and P, however the short primers were both forward and reverse primers.</p><br><br>
+included restriction sites S and P, however the short primers were both forward and reverse primers.<br><br>
+Primers:<br>
+GUN4-F1          AAGCGCAACTGGGTTTACTTC<br>
+GUN4-R1S        ATACAACACCTGGCAGGATCA<br>
+GUN4-R1L        CAGCGGCGGCCTACTAGTATACAACACCTGGCAGG<br>
+ChlM-F1           AGACGGTGGACAAGGTGCT<br>
+CHLM-R1S       GTCCGAGTCCATCAGTCCTTAC<br>
+CHLM-R1L       CAGCGGCCGCCTACTAGTCCGAGTCCATCAGTCC<br>
+ChlD-F1            CCCGTGGAAGACCAAGATGC<br>
+ChlD-R1S         GTAACGCTCACATACCAACAC<br>
+ChlD-R1L         CAGCGGCCGCCTACTAGTAACGCTCACATACCAAC<br>
+Chll1-F1           AGCTGATGAGCGAGGAGGT<br>
+Chll1-R1S         TGCCGCTTACTCCATGCCG<br>
+Chll1-R1L         CAGCGGCCGCCTACTAGTGCCGCTGACTCCATG<br>
+CTH1-F1           CGGAGATGGTCAACGACTG<br>
+CTH-R1S           GCTCCAAAGCACTCTCAAAACT<br>
+CTHR1L             CAGCGGCCGCCTACTAGTGCTCCAAAGCACTCTC<br>
+ChlH-F1            GCTCATCTTCATTGAGGAGCTT<br>
+ChlH-R1            GCTGTTCACGAAGTTCTTG<br>
+ChlH-F2            GAGGATCTGATCCAGTCGGT<br>
+ChlH-R2            CTGGTCAACGTCAGCCAGGA<br>
+ChlH-F3            GAGATGTACCTGAAGCGCAAG<br>
+ChlH-R3S          ACTAGTGCTACCATGAAGGG<br>
+ChlH-R3L          CAGCGGCCGCCTACTAGTGCTACCATGAAGGG<br>
+POR-F1             ACTCAATCCTGCACCTGGAC<br>
+POR-R1S           CAGAGACGAACCGCAGGTAG<br>
+POR-R1L           CAGCGGCCGCCTACTAGTCAGAGACGAACCGCAG<br>