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Team:British Columbia/Notebook/Week 7
From 2011.igem.org
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| + | <b>Week 7: July 17-23</b> | ||
| - | + | ==Human Practices== | |
<html><a title='By Iwona Erskine-Kellie (Flickr) [CC-BY-2.0 (www.creativecommons.org/licenses/by/2.0)], via Wikimedia Commons' href='http://commons.wikimedia.org/wiki/File:Science_World_Sunset.jpg'><img height='200' alt='Science World Sunset' src='http://upload.wikimedia.org/wikipedia/commons/thumb/a/a0/Science_World_Sunset.jpg/800px-Science_World_Sunset.jpg'/></a></html> | <html><a title='By Iwona Erskine-Kellie (Flickr) [CC-BY-2.0 (www.creativecommons.org/licenses/by/2.0)], via Wikimedia Commons' href='http://commons.wikimedia.org/wiki/File:Science_World_Sunset.jpg'><img height='200' alt='Science World Sunset' src='http://upload.wikimedia.org/wikipedia/commons/thumb/a/a0/Science_World_Sunset.jpg/800px-Science_World_Sunset.jpg'/></a></html> | ||
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Laura was very excited to meet with Mrs. Anderson on Monday to discuss our teams involvement in the Future Science Leaders program at Science World! Science World British Columbia is a non-profit organization which engages British Columbians in science and inspires future science and technology leadership throughout our province. The Future Science Leaders is a program offered to high school students who are keen and bright and want to further their understanding of science. Through weekly meetings the program will cover several difference sciences such as biology, mathematics, technology, physical sciences, earth and space, and technology. We as an iGEM team have the privilege of presenting our project to this group of high school students and their parents. We will also be educating the students on the diverse applications of synthetic biology and give a brief tutorial about what synthetic biology is! There is also an opportunity to promote the idea of a high school iGEM team for next year. | Laura was very excited to meet with Mrs. Anderson on Monday to discuss our teams involvement in the Future Science Leaders program at Science World! Science World British Columbia is a non-profit organization which engages British Columbians in science and inspires future science and technology leadership throughout our province. The Future Science Leaders is a program offered to high school students who are keen and bright and want to further their understanding of science. Through weekly meetings the program will cover several difference sciences such as biology, mathematics, technology, physical sciences, earth and space, and technology. We as an iGEM team have the privilege of presenting our project to this group of high school students and their parents. We will also be educating the students on the diverse applications of synthetic biology and give a brief tutorial about what synthetic biology is! There is also an opportunity to promote the idea of a high school iGEM team for next year. | ||
| - | + | ==3-Carene== | |
| - | [[File:Marijacob2.JPG]] | + | [[File:Marijacob1.JPG | thumb | right | 200px | Jacob working away]] |
| + | Daisy has been trying to put the his-tagged truncated 3-carene synthase into the yeast plasmid, PA415GPD. This has been more difficult than anticipated. The primers used to PCR out the truncated 3-carene synthase seem to produce a smear around 1.7 kb. This is the correct size range for the truncated synthase but it is not a clear band. Daisy may need to adjust the annealing temperature of her primers to get a specific band. At this point, she is going to digest and ligate this non-specific band into the yeast plasmid. She will try purification methods of gel extraction and PCR purification... | ||
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| + | ==1,8-cineole== | ||
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| + | Jacob's sequencing also came back null. However, the restriction digest gels clearly showed that there were no cut sites in the synthase, so Jacob decided to try getting the synthases into biobrick plasmids. Three PCR attempts later... | ||
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| + | ==Beta-pinene== | ||
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| + | [[File:Marijacob2.JPG | thumb | left | 150px |Marianne and Jacob share their frustrations]] | ||
Marianne's sequencing attempts failed. Very frustrated at this point, she decided that she doesn't want to waste any more time on sequencing. So she restriction digested the mini-prepped plasmids to see if the site is still there. Gel verification of the digests suggested that the site has been removed (the gel showed bands identical to the uncut plasmid). | Marianne's sequencing attempts failed. Very frustrated at this point, she decided that she doesn't want to waste any more time on sequencing. So she restriction digested the mini-prepped plasmids to see if the site is still there. Gel verification of the digests suggested that the site has been removed (the gel showed bands identical to the uncut plasmid). | ||
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Marianne started to assemble the biobrick part. She digested the linearized psb1C3 and the synthase gene with EcoRI and PstI using Biobrick Restriction Digest protocol. She then ligated the backbone and the part and transformed it into DH5alpha competent cells. Colony PCR of transformants using G1004 and G1005 primers resulted in no bands on the gel... Therefore, she repeated the PCR using a new batch of primers as well as a different primer pair VF2/VR. | Marianne started to assemble the biobrick part. She digested the linearized psb1C3 and the synthase gene with EcoRI and PstI using Biobrick Restriction Digest protocol. She then ligated the backbone and the part and transformed it into DH5alpha competent cells. Colony PCR of transformants using G1004 and G1005 primers resulted in no bands on the gel... Therefore, she repeated the PCR using a new batch of primers as well as a different primer pair VF2/VR. | ||
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Marianne also restriction digested the yeast plasmids and synthase genes and ligated the following 8 combinations: | Marianne also restriction digested the yeast plasmids and synthase genes and ligated the following 8 combinations: | ||
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Marianne then transformed the ligated samples. Marianne had a very long day... | Marianne then transformed the ligated samples. Marianne had a very long day... | ||
| - | + | ==(-)-limonene== | |
| - | PCR of the synthase using yeast primers resulted in 4 bands on the gel. Troubleshooting: use a temperature gradient from 64oC to 72oC... | + | PCR of the synthase using yeast primers resulted in 4 bands on all the lanes the gel. |
| + | *Troubleshooting: use a temperature gradient from 64oC to 72oC... Result: 4 bands again. | ||
| + | *More troubleshooting: decrease the extension time to 30sec (15sec/1kb) with an annealing temperature of 70C. Vicki will also transform original plasmid (pADM743) into DH5alpha cells in case the plasmid she is working with has been contaminated somehow, and hence not being PCRed off properly. | ||
| - | Vicki decided to get new primers to re-attempt the SDM... but once again, there were no bands. | + | Vicki decided to get new primers (higher temperature and more base pairs to anneal to the template) to re-attempt the SDM... but once again, there were no bands. Vicki is extremely frustrated at this point, and is starting to doubt the integrity of the original tube (pADM743) of (-)-limonene synthase. |
| - | + | ==ERG20== | |
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Since they still hadn't received the plasmids from France, Gurpal decided to try generating the erg20-2 mutant by SDM. After ordering and receiving primers, his goal was to isolate the ERG20 gene from wild type yeast. Three tubes were prepared for the PCR, each containing a different amount of yeast genome, and the PCR was performed. Afterwards, Jacob ran gel electrophoresis to see if the PCR worked. However, the gel showed nothing but the ladder... | Since they still hadn't received the plasmids from France, Gurpal decided to try generating the erg20-2 mutant by SDM. After ordering and receiving primers, his goal was to isolate the ERG20 gene from wild type yeast. Three tubes were prepared for the PCR, each containing a different amount of yeast genome, and the PCR was performed. Afterwards, Jacob ran gel electrophoresis to see if the PCR worked. However, the gel showed nothing but the ladder... | ||
Fortunately, the ERG20 and erg20-2 genes arrived from France on pNEV-N plasmids the next day! This increased the entire team's morale 10-fold! The ERG20 gene was on the pBS plasmid and the erg20-2 was on the pKS plasmid. Gurpal successfully transformed these plasmids into <i>E. coli</i> on his second attempt using newly made Ampicillin agar plates. These plasmids were also verified by gel electrophoresis. | Fortunately, the ERG20 and erg20-2 genes arrived from France on pNEV-N plasmids the next day! This increased the entire team's morale 10-fold! The ERG20 gene was on the pBS plasmid and the erg20-2 was on the pKS plasmid. Gurpal successfully transformed these plasmids into <i>E. coli</i> on his second attempt using newly made Ampicillin agar plates. These plasmids were also verified by gel electrophoresis. | ||
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Revision as of 06:19, 8 August 2011
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Contents |
Human Practices
Laura was very excited to meet with Mrs. Anderson on Monday to discuss our teams involvement in the Future Science Leaders program at Science World! Science World British Columbia is a non-profit organization which engages British Columbians in science and inspires future science and technology leadership throughout our province. The Future Science Leaders is a program offered to high school students who are keen and bright and want to further their understanding of science. Through weekly meetings the program will cover several difference sciences such as biology, mathematics, technology, physical sciences, earth and space, and technology. We as an iGEM team have the privilege of presenting our project to this group of high school students and their parents. We will also be educating the students on the diverse applications of synthetic biology and give a brief tutorial about what synthetic biology is! There is also an opportunity to promote the idea of a high school iGEM team for next year.
3-Carene
Daisy has been trying to put the his-tagged truncated 3-carene synthase into the yeast plasmid, PA415GPD. This has been more difficult than anticipated. The primers used to PCR out the truncated 3-carene synthase seem to produce a smear around 1.7 kb. This is the correct size range for the truncated synthase but it is not a clear band. Daisy may need to adjust the annealing temperature of her primers to get a specific band. At this point, she is going to digest and ligate this non-specific band into the yeast plasmid. She will try purification methods of gel extraction and PCR purification...
1,8-cineole
Jacob's sequencing also came back null. However, the restriction digest gels clearly showed that there were no cut sites in the synthase, so Jacob decided to try getting the synthases into biobrick plasmids. Three PCR attempts later...
Beta-pinene
Marianne's sequencing attempts failed. Very frustrated at this point, she decided that she doesn't want to waste any more time on sequencing. So she restriction digested the mini-prepped plasmids to see if the site is still there. Gel verification of the digests suggested that the site has been removed (the gel showed bands identical to the uncut plasmid).
Marianne PCRed off the original and the SDMed synthase using yeast primers (containing XhoI and SpeI restriction enzyme sites) in order to put it in the yeast plasmid PA415GPD. Marianne also PCRed off the SDMed synthase using biobrick primers (containing EcoRI, XbaI, SpeI, PstI restriction enzyme sites) to put it in the psb1C3 backbone. Gel verification for both PCRs shows bands at the correct length!
Marianne started to assemble the biobrick part. She digested the linearized psb1C3 and the synthase gene with EcoRI and PstI using Biobrick Restriction Digest protocol. She then ligated the backbone and the part and transformed it into DH5alpha competent cells. Colony PCR of transformants using G1004 and G1005 primers resulted in no bands on the gel... Therefore, she repeated the PCR using a new batch of primers as well as a different primer pair VF2/VR.
Marianne also restriction digested the yeast plasmids and synthase genes and ligated the following 8 combinations:
- original + his-tagged + GAL
- original + his-tagged + GDP
- original + no-his + GAL
- original + no-his + GDP
- SDM + his-tagged + GAL
- SDM + his-tagged + GDP
- SDM + no-his + GAL
- SDM + no-his + GDP
Marianne then transformed the ligated samples. Marianne had a very long day...
(-)-limonene
PCR of the synthase using yeast primers resulted in 4 bands on all the lanes the gel.
- Troubleshooting: use a temperature gradient from 64oC to 72oC... Result: 4 bands again.
- More troubleshooting: decrease the extension time to 30sec (15sec/1kb) with an annealing temperature of 70C. Vicki will also transform original plasmid (pADM743) into DH5alpha cells in case the plasmid she is working with has been contaminated somehow, and hence not being PCRed off properly.
Vicki decided to get new primers (higher temperature and more base pairs to anneal to the template) to re-attempt the SDM... but once again, there were no bands. Vicki is extremely frustrated at this point, and is starting to doubt the integrity of the original tube (pADM743) of (-)-limonene synthase.
ERG20
Since they still hadn't received the plasmids from France, Gurpal decided to try generating the erg20-2 mutant by SDM. After ordering and receiving primers, his goal was to isolate the ERG20 gene from wild type yeast. Three tubes were prepared for the PCR, each containing a different amount of yeast genome, and the PCR was performed. Afterwards, Jacob ran gel electrophoresis to see if the PCR worked. However, the gel showed nothing but the ladder...
Fortunately, the ERG20 and erg20-2 genes arrived from France on pNEV-N plasmids the next day! This increased the entire team's morale 10-fold! The ERG20 gene was on the pBS plasmid and the erg20-2 was on the pKS plasmid. Gurpal successfully transformed these plasmids into E. coli on his second attempt using newly made Ampicillin agar plates. These plasmids were also verified by gel electrophoresis.
