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Team:Imperial College London/Notebook/week3
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| - | + | <h2>Week 3: 18th July to 24th July</h2> | |
| - | + | <h3>Monday, 18th July</h3> | |
| + | <p>We had a pretty productive day starting on Project Auxin. Ming, totally out of the blue, shows up with some phytogels that he seeded with Arabidopsis, a fantastic start to any plant project. <br /> | ||
| + | Nikki and Frank went over the presentation 3 or 4 times until it was ready to give to the team from BBC’s Horizon at 11:30. In the meantime, everyone hit the research hard, looking for genes and setting up appointments to speak to experts. <br /> | ||
| + | At 2pm we moved into our new labs in the Sir Alexander Fleming building, where we got a brief safety introduction and began ordering the equipment we were likely to need in the coming weeks. Claire from LSE sent over a list of questions that we have to take into consideration for the human practices aspect of our project. <br /> | ||
| + | Nina, Yuanwei and Si also got started on some modelling, doing some pretty impressive MatLab stuff whilst the rest of us started designing experiments that would be needed to test our system, module by module. Nikki also got started on emailing newspapers and magazines as part of our outreach goals. </p> | ||
| - | + | <h3>Tuesday, 19th July</h3> | |
| - | < | + | <p>Ming and Rebekka met Thorsten Hamann to discuss how to grow Arabidopsis in liquid culture. A problem will be organising DR5 seeds but hopefully someone will be able to help us out. They also got an induction to the plant facilities at Imperial and will hopefully be ready to start seeding soon!<br /> |
| - | + | <br /> | |
| - | <br> | + | Lab supplies were organised and ordered and will hopefully arrive soon.<br /> |
| - | + | <br /> | |
| - | <br> | + | The auxin and chemotaxis teams are working on the genetic constructs and should have them ready by tomorrow morning. Most of the optimisation is now done and sequences are almost ready to be ordered.<br /> |
| - | + | <br /> | |
| - | <br> | + | The chemotaxis team met with the local chemotaxis expert and got some valuable modelling advice and some general context for the chemotaxis issue. Modelling the feedback loop in chemotaxis is now a lot more advanced.<br /> |
| - | + | <br /> | |
| - | </ | + | A couple of us met CJ from the Royal College of Art to discuss design and outreach options for the project. She and Koby will be working with us and we are looking forward to their artistic input! </p> |
| - | + | <h3>Wednesday, 20th July</h3> | |
| - | < | + | <p>Arabidopsis team : Ming and Rebekka were informed that the DR5-GFP seed was available at ABRC. Rebekka continued her human practise discussion and assigned different tasks to the team while Ming was preparing liquid media and sterilizing WT arabidopsis seeds for seeding in the next day. ~ Thanks to P' Khaow ; Ms Issariya who has helped us with the protocol and the wetlab. :) <br /> |
| - | Ming and Rebekka | + | <br /> |
| + | Auxin team : Chris and Nikki were finding the sequences in the morning along with discussing about the project direction and cloning strategies. They also looked for <i>Pseudomonas syringae</i> and found stock at retail which needs to be PCR'd if synthetic parts do not arrive <br /> | ||
| + | <br /> | ||
| + | Chemotaxis team : Frank designed the kill switch but not all parts were available. He also designed the agar plate assay and work on a capillary chemotaxis assay. Nick was working on a gene construct where he figured out the RBS sequences, optimised sequences, generated constructs in serial cloner, and join human practise talk with Rebekka. <br /> | ||
| + | <br /> | ||
| + | Modelling team : Nina and Si used Matlab to model the distribution pattern of malate and citrate concerning initial concentrations and concentrations at different distances. Also they were progressing on the chemotaxis pathway modelling.<br /> | ||
| + | <br /> | ||
| + | Wiki : Yuanwei re-designed the team page and uploaded more photos.</p> | ||
| - | + | <h3>Thursday, 21st July</h3> | |
| + | <p>Arabidopsis team: Rebekka has been doing some research on human practices. Claire's e-mail has been very helpful in that it has allowed us to see that containment is not the only option that should be considered. We will be trying to also consider what effects our bacteria might have if containment fails. Ming finished seeding the Arabidopsis seeds into the liquid media. He also did some research with Nikki on soil erosion in Asia as well as some research into the MB aspect of human practices (how GM bacteria might affect other bacterial populations).<br /> | ||
| + | <br /> | ||
| + | Auxin team: Nikki did some research on soil erosion and desertification. She also worked on the second version of the project description and also started preparing the progress report presentation that was due on the following day. Chris worked on the DNA sequences for the auxin module as well as for the Dendra2 gene. These sequences should also be sent for synthesis early next week.<br /> | ||
| + | <br /> | ||
| + | Chemotaxis team: Nicolas was working on the chemotaxis module's DNA sequences to be sent off for synthesis early next week. Meanwhile, Frank tried to design experiments to perform for the chemotaxis module as well as working on a kill switch for the bacteria. He was playing with the idea of using a UV sensitive promoter for it.<br /> | ||
| + | <br /> | ||
| + | Modelling team: Si and Nina met Dr. Endres to talk about modeling chemotaxis. They then made a model for single cell chemotaxis and found out that the bacteria reacts optimally to 10-6M malate concentrations.<br /> | ||
| + | <br /> | ||
| + | Wiki: Yuanwei continued to work hard on the wiki. We agreed on how the wiki should be organised and Yuanwei will upload the cool new menu very soon.</p> | ||
| - | + | <h3>Friday, 22nd July</h3> | |
| + | <p>We had presentation update for Professor Kitney and he provided us with a number of relevant points, which will help us to further improve the project. <br /> | ||
| + | Arabidopsis team: Rebekka has continued research into the human practice. Ming was continuing seeding Arabidopsis. <br /> | ||
| + | Auxin team: Nikki was working mainly on the presentation and then continued researching our problem of soil erosion and desertification. Chris, James and Dr Ellis were finalising sequences for order, particularly RBS sequences, which they were generating using RBS Salis and Voigt calculators. <br /> | ||
| + | Chemotaxis team: Frank was helping Nikki with the presentation and then was looking into inducible promoters for a kill-switch, which we will have to introduce into our system. Nick was finalising sequences for order, conrolling all the sequences for errors and illegal restriction sites. <br /> | ||
| + | Modelling team: Nina and Si have continued modelling of bacterial chemotaxis as a flux and have met Dr Siggers to talk about modelling of chemotaxis. <br /> | ||
| + | Wiki: Yuanwei was working on the wiki as usual. <br /> | ||
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Latest revision as of 17:02, 15 September 2011
Diary
This is our diary page which records the daily activities of the team. Click on the links below to see a summary of events and activities happening each week.
Week 3: 18th July to 24th July
Monday, 18th July
We had a pretty productive day starting on Project Auxin. Ming, totally out of the blue, shows up with some phytogels that he seeded with Arabidopsis, a fantastic start to any plant project.
Nikki and Frank went over the presentation 3 or 4 times until it was ready to give to the team from BBC’s Horizon at 11:30. In the meantime, everyone hit the research hard, looking for genes and setting up appointments to speak to experts.
At 2pm we moved into our new labs in the Sir Alexander Fleming building, where we got a brief safety introduction and began ordering the equipment we were likely to need in the coming weeks. Claire from LSE sent over a list of questions that we have to take into consideration for the human practices aspect of our project.
Nina, Yuanwei and Si also got started on some modelling, doing some pretty impressive MatLab stuff whilst the rest of us started designing experiments that would be needed to test our system, module by module. Nikki also got started on emailing newspapers and magazines as part of our outreach goals.
Tuesday, 19th July
Ming and Rebekka met Thorsten Hamann to discuss how to grow Arabidopsis in liquid culture. A problem will be organising DR5 seeds but hopefully someone will be able to help us out. They also got an induction to the plant facilities at Imperial and will hopefully be ready to start seeding soon!
Lab supplies were organised and ordered and will hopefully arrive soon.
The auxin and chemotaxis teams are working on the genetic constructs and should have them ready by tomorrow morning. Most of the optimisation is now done and sequences are almost ready to be ordered.
The chemotaxis team met with the local chemotaxis expert and got some valuable modelling advice and some general context for the chemotaxis issue. Modelling the feedback loop in chemotaxis is now a lot more advanced.
A couple of us met CJ from the Royal College of Art to discuss design and outreach options for the project. She and Koby will be working with us and we are looking forward to their artistic input!
Wednesday, 20th July
Arabidopsis team : Ming and Rebekka were informed that the DR5-GFP seed was available at ABRC. Rebekka continued her human practise discussion and assigned different tasks to the team while Ming was preparing liquid media and sterilizing WT arabidopsis seeds for seeding in the next day. ~ Thanks to P' Khaow ; Ms Issariya who has helped us with the protocol and the wetlab. :)
Auxin team : Chris and Nikki were finding the sequences in the morning along with discussing about the project direction and cloning strategies. They also looked for Pseudomonas syringae and found stock at retail which needs to be PCR'd if synthetic parts do not arrive
Chemotaxis team : Frank designed the kill switch but not all parts were available. He also designed the agar plate assay and work on a capillary chemotaxis assay. Nick was working on a gene construct where he figured out the RBS sequences, optimised sequences, generated constructs in serial cloner, and join human practise talk with Rebekka.
Modelling team : Nina and Si used Matlab to model the distribution pattern of malate and citrate concerning initial concentrations and concentrations at different distances. Also they were progressing on the chemotaxis pathway modelling.
Wiki : Yuanwei re-designed the team page and uploaded more photos.
Thursday, 21st July
Arabidopsis team: Rebekka has been doing some research on human practices. Claire's e-mail has been very helpful in that it has allowed us to see that containment is not the only option that should be considered. We will be trying to also consider what effects our bacteria might have if containment fails. Ming finished seeding the Arabidopsis seeds into the liquid media. He also did some research with Nikki on soil erosion in Asia as well as some research into the MB aspect of human practices (how GM bacteria might affect other bacterial populations).
Auxin team: Nikki did some research on soil erosion and desertification. She also worked on the second version of the project description and also started preparing the progress report presentation that was due on the following day. Chris worked on the DNA sequences for the auxin module as well as for the Dendra2 gene. These sequences should also be sent for synthesis early next week.
Chemotaxis team: Nicolas was working on the chemotaxis module's DNA sequences to be sent off for synthesis early next week. Meanwhile, Frank tried to design experiments to perform for the chemotaxis module as well as working on a kill switch for the bacteria. He was playing with the idea of using a UV sensitive promoter for it.
Modelling team: Si and Nina met Dr. Endres to talk about modeling chemotaxis. They then made a model for single cell chemotaxis and found out that the bacteria reacts optimally to 10-6M malate concentrations.
Wiki: Yuanwei continued to work hard on the wiki. We agreed on how the wiki should be organised and Yuanwei will upload the cool new menu very soon.
Friday, 22nd July
We had presentation update for Professor Kitney and he provided us with a number of relevant points, which will help us to further improve the project.
Arabidopsis team: Rebekka has continued research into the human practice. Ming was continuing seeding Arabidopsis.
Auxin team: Nikki was working mainly on the presentation and then continued researching our problem of soil erosion and desertification. Chris, James and Dr Ellis were finalising sequences for order, particularly RBS sequences, which they were generating using RBS Salis and Voigt calculators.
Chemotaxis team: Frank was helping Nikki with the presentation and then was looking into inducible promoters for a kill-switch, which we will have to introduce into our system. Nick was finalising sequences for order, conrolling all the sequences for errors and illegal restriction sites.
Modelling team: Nina and Si have continued modelling of bacterial chemotaxis as a flux and have met Dr Siggers to talk about modelling of chemotaxis.
Wiki: Yuanwei was working on the wiki as usual.
