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Team:Calgary/17 July 2009
From 2009.igem.org
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3. Invitrogen T4 Ligase at room temperature (~21<sup>o</sup>C) for one week | 3. Invitrogen T4 Ligase at room temperature (~21<sup>o</sup>C) for one week | ||
* The Quick Ligated product was transformed into Top 10 cells and was grown on LB plates with Kan resistance for 16 hours. | * The Quick Ligated product was transformed into Top 10 cells and was grown on LB plates with Kan resistance for 16 hours. | ||
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| - | Watched the Awesome Molecular biology video . Learned quite a bit about cells in our body . Set up Matlab so that when data is present the Hill Equation will automatically fit the data to a curve . | + | Watched the Awesome Molecular biology video. Learned quite a bit about cells in our body . Set up Matlab so that when data is present the Hill Equation will automatically fit the data to a curve . |
At the end of the Day we had a fire alarm. | At the end of the Day we had a fire alarm. | ||
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| - | *Today I sent one of the colonies from my restriction digest yesterday down for sequencing. When these results come in, we will be able to see if the B0015 terminator has been successfully cloned into the J13002-LuxOD47E construct. If this is | + | *Today I sent one of the colonies from my restriction digest yesterday down for sequencing. When these results come in, we will be able to see if the B0015 terminator has been successfully cloned into the J13002-LuxOD47E construct. If this is successful, my circuit will be done! From here, I can use the parts that Kevin has been constructing with GFP to put my circuit in and test the functioning of my circuit. |
*This afternoon I helped Mandy with editing more photos for the Wiki. I also looked about CedarLane Laboratories, our sponsor of the month, and wrote a short paragraph about them to include on our Wiki. I also sent an Ethics paper that Fahd sent me. | *This afternoon I helped Mandy with editing more photos for the Wiki. I also looked about CedarLane Laboratories, our sponsor of the month, and wrote a short paragraph about them to include on our Wiki. I also sent an Ethics paper that Fahd sent me. | ||
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5) Read Ethics papers | 5) Read Ethics papers | ||
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Our Framework is able to produce more results than concentration graphs. Concentration graphs are good to observe the general trends in the system and to gain some numerical data, however there are better ways to present the patterns and trends in our model. For example, we could use matrixes and arrays to show the change of concentration of given agents over the simulation period using colors. | Our Framework is able to produce more results than concentration graphs. Concentration graphs are good to observe the general trends in the system and to gain some numerical data, however there are better ways to present the patterns and trends in our model. For example, we could use matrixes and arrays to show the change of concentration of given agents over the simulation period using colors. | ||
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An interesting example would be: AI-2 Binding to the LuxP-LuxQ Protein Complex. | An interesting example would be: AI-2 Binding to the LuxP-LuxQ Protein Complex. | ||
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Each column represents one of twenty E.coli bacteria. The state of the modelled bacteria over a period of 50 simulated time steps is depicted along the vertical axis. The color of each cell indicates the binding degree between AI-2 and the LuxP-LuxQ complex. The color spectrum spans from red (no binding) over white to blue (complete binding). As time progresses an increasing amount of AI-2 is produced by LuxS and gets bound to LuxP-LuxQ. | Each column represents one of twenty E.coli bacteria. The state of the modelled bacteria over a period of 50 simulated time steps is depicted along the vertical axis. The color of each cell indicates the binding degree between AI-2 and the LuxP-LuxQ complex. The color spectrum spans from red (no binding) over white to blue (complete binding). As time progresses an increasing amount of AI-2 is produced by LuxS and gets bound to LuxP-LuxQ. | ||
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That is what I have been working on this week. As usual I had 2 meetings to go as well. | That is what I have been working on this week. As usual I had 2 meetings to go as well. | ||
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Purpose: to perform plasmid isolation in order to proceed with sequencing/restriction digest for sequence verification. The plasmid isolation was done using the QIAprep Spin MiniPrep Kit (QIAGEN). Plasmid purity and concentration were measured using the NanoDrop Spectrophotometer. After isolation, colony 3 was sent to the University of Calgary DNA Sequencing Facility with BBK CP F/R and R0040-Reverse primers. | Purpose: to perform plasmid isolation in order to proceed with sequencing/restriction digest for sequence verification. The plasmid isolation was done using the QIAprep Spin MiniPrep Kit (QIAGEN). Plasmid purity and concentration were measured using the NanoDrop Spectrophotometer. After isolation, colony 3 was sent to the University of Calgary DNA Sequencing Facility with BBK CP F/R and R0040-Reverse primers. | ||
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| - | Basic instructions for construction and bacterial transformation have been completed, which I will still have to add to the touch_start event or have them beside the activity. The bacterial transformation quiz also had to be able to be reset at any time so each question for the quiz now has a reset button for a choice and when touched, it will not only reset any variables for the quiz, but reset the progress test tube to the original white/transparent colour | + | Basic instructions for construction and bacterial transformation have been completed, which I will still have to add to the touch_start event or have them beside the activity. The bacterial transformation quiz also had to be able to be reset at any time so each question for the quiz now has a reset button for a choice and when touched, it will not only reset any variables for the quiz, but reset the progress test tube to the original white/transparent colour. |
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I have isolated the plasmids from these overnight cultures, and the purity and concentration of them were measured using nanodrop. They were pure enough to move on with. | I have isolated the plasmids from these overnight cultures, and the purity and concentration of them were measured using nanodrop. They were pure enough to move on with. | ||
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| - | Since our Luciferase did not turn out great, we turned our attention to GFP:LVA. But because the part with GFP:LVA does not contain RBS, I need to | + | Since our Luciferase did not turn out great, we turned our attention to GFP:LVA. But because the part with GFP:LVA does not contain RBS, I need to construct <i>Pqrr4</i>+B0034 first. <i>Pqrr4</i> was cut with SpeI+PstI and B0034 was cut with XbaI+PstI. <i>Pqrr4</i> was then phosphatase treated, and the two were ligated together. The ligated product was finally transformed into TOP10 cells. Carol promised to take the plates out tomorrow. |
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| - | In the activity now, users can take cells, suspend them and then add the appropriate enzymes to lyse cells and degrade proteins … Then the solution is poured into a cartridge and eluted…etc. For this activity, a couple of the test tubes used have Katie’s inventory script, which means you have to drop things in | + | In the activity now, users can take cells, suspend them and then add the appropriate enzymes to lyse cells and degrade proteins … Then the solution is poured into a cartridge and eluted…etc. For this activity, a couple of the test tubes used have Katie’s inventory script, which means you have to drop things in e.g. the suspended cells, the proteinase, etc. Dialogue menus (like clicking buttons to choose) are used to identify what cells are being used (haven’t fully implemented this yet), what step is being centrifuged, etc. The entire system works around the centrifuge. I still need to make sure the instructions given at every step are clear, and need to finish the notecard that should give a thorough explanation of extraction. :D |
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Next week, I will also coordinate with Katie so that we figure out what the combinations of lab activities can be done, and how many ‘types’ of the same activity can be done (eg. PCR of different parts, etc.) depending on the design of the remaining 2 lab missions. (I got half way through the design of the hardest one before I got sidetracked by realizing that we should have DNA extraction as an activity). | Next week, I will also coordinate with Katie so that we figure out what the combinations of lab activities can be done, and how many ‘types’ of the same activity can be done (eg. PCR of different parts, etc.) depending on the design of the remaining 2 lab missions. (I got half way through the design of the hardest one before I got sidetracked by realizing that we should have DNA extraction as an activity). | ||
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| - | For wiki, I made a couple icons, that will serve as a visual ‘reminder’ of what section you’re in the wiki for (icon for lab work, icon for modelling, icon for ethics, etc.) Because although the site design is cohesive ( | + | For wiki, I made a couple icons, that will serve as a visual ‘reminder’ of what section you’re in the wiki for (icon for lab work, icon for modelling, icon for ethics, etc.) Because although the site design is cohesive (e.g. practically looks the same on every page), other than the header, there should be other things that serve as a reminder for where you are, especially if the page scrolls vertically a lot. |
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| - | After the marketing meeting, I contact | + | After the marketing meeting, I contact SemBioSys, called up the Investor Relations Inquires lead, Abby Garfunkel and told her about our project. She asked me to mail her the sponsorship pkg so she could forward it to Dr. Moloney. I wrote an email to Dr. Moloney restating our project goal, meeting and that I spoke to Abby. The rest of the marketing team checked over the email before I sent it out. Hopefully, he gets back to me soon or I’ll call Ms. Abby again on Tuesday. |
I found a number for Jay Ingram but I couldn’t find any emails anywhere on the websites. However, I spoke to Dr. Jacob today and he said he knew Mr. Ingram and his wife and he’ll send me her email address and hopefully I can get a hold of him through her. I started writing the email that I’m going to send to Jay Ingram. Dr. Jacob wanted to know how we’re doing in marketing so I told him everything and about our marketing meeting this morning. | I found a number for Jay Ingram but I couldn’t find any emails anywhere on the websites. However, I spoke to Dr. Jacob today and he said he knew Mr. Ingram and his wife and he’ll send me her email address and hopefully I can get a hold of him through her. I started writing the email that I’m going to send to Jay Ingram. Dr. Jacob wanted to know how we’re doing in marketing so I told him everything and about our marketing meeting this morning. | ||
| - | Oh and I sent Mandel Scientific an email asking for a | + | Oh and I sent Mandel Scientific an email asking for a pipette set and pipette tips. So next week, I have to follow-up with a WHOLE BUNCH OF companies (about 10 –practically all the ones I’ve mentioned over the past 2 days). I also updated the iGEM marketing company list on gmail spreadsheet. |
Finally, I just helped Jamie with plating after he transformed Cl lambda earlier today. | Finally, I just helped Jamie with plating after he transformed Cl lambda earlier today. | ||
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| - | The purpose of this meeting was to flesh out a procedure for attacking | + | The purpose of this meeting was to flesh out a procedure for attacking characterization. We decided that the six areas we looked at yesterday and earlier today were all feasible to test, and it looks like most of the evaluation can be done with SimBiology and the optimisation toolboxes, both of which we have on our own computers. We also explored other areas that might be interesting, such as the circuit behaviour in different conditions (ie, vary the temperature or the medium composition and see what happens). It’ll definitely be a lot of work to test all of this, but if we plan our procedures well, we should be able to see results. |
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I searched online for an AI-2 supplier, as well as molecules that might mimic its behaviour as well as any corporation that might supply those. I found a series of mimics (mostly variants of AI-2), each of which were patented by the Bassler lab. At that point, I decided that it would be best for us to just e-mail the Bassler lab and find out where they get their AI-2 molecules. | I searched online for an AI-2 supplier, as well as molecules that might mimic its behaviour as well as any corporation that might supply those. I found a series of mimics (mostly variants of AI-2), each of which were patented by the Bassler lab. At that point, I decided that it would be best for us to just e-mail the Bassler lab and find out where they get their AI-2 molecules. | ||
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Revision as of 22:43, 20 October 2009
UNIVERSITY OF CALGARY
