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| - | June 26, 2009
| + | JUNE 26, 2009 |
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| - | Descriptive Title of What You’re Doing
| + | Preparation of Meeting |
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| - | WIKI CODING HERE
| + | * Prepared for team meeting |
| | + | * From the sequencing results of the forward and reverse reaction, the results did not confirm the sequence for <i>luxCDABE</i>. We decided to continue with biobrick cloning. |
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| - | Stochastic Models of Gene Expression | + | *Stochastic Models of Gene Expression |
| - | <br>Stochastic mechanisms in gene expression
| + | *Stochastic mechanisms in gene expression |
| - | <br>A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways --- has stochastic rate constants
| + | *A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways --- has stochastic rate constants |
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| - | Descriptive Title of What You're Doing
| + | Ligation and Transformation of BBK LuxOD47E and the psB1AC3 Vector Take Two! |
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| - | WIKI CODING HERE
| + | *Today there was no growth on the plates that I made yesterday, so I will have to re-ligate and transform as the Bacteria were not able to uptake the DNA for whatever reason. |
| | + | *I followed ligation and transformationn protocols using the BBK LuxOD47E and the psB1AC3 vector that I digested previously. Once transformed, I plated this on C plates and left in the incubator for overnight growth. |
| | + | *Today I also prepared for and partipated in our weekly team meeting, where each subgroup talked about their progress up to date, specifically what they accomplished this past week and what they plan to do next week. |
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| - | Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project | + | Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project. |
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| | Graph section of our model is completed this week. As it was mentioned, now we have two general types of graphs, one showing the change of concentration of an element in all the cells, and the other one shows the change of concentration of an element in each cell. There is a menu designed in result section that users can use to choose which one of these types of graphs they would like to observe. | | Graph section of our model is completed this week. As it was mentioned, now we have two general types of graphs, one showing the change of concentration of an element in all the cells, and the other one shows the change of concentration of an element in each cell. There is a menu designed in result section that users can use to choose which one of these types of graphs they would like to observe. |
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| | This week, I also had a meeting with the other modeling team and we compared our models together. As a result of that meeting, we had to change and edit some of our evolution rules. Changing a rule in this model could not be done easily. When a rule changes, many functions should change too. For instance, some functions read rules and calculate the possibilities of their applications. Other functions apply the rules to the environment by eliminating the reactants and adding products. Therefore, I spent some time this week to edit the existing rules and adding the new rules asked by Thane and the equation based modeling group. Another important aspect that was discussed in the meeting was “DIVISION”. I have started to implement this function to our model. This function should get an environment as input and applies division to the environment and pass the new environment with double number of cells as its output. | | This week, I also had a meeting with the other modeling team and we compared our models together. As a result of that meeting, we had to change and edit some of our evolution rules. Changing a rule in this model could not be done easily. When a rule changes, many functions should change too. For instance, some functions read rules and calculate the possibilities of their applications. Other functions apply the rules to the environment by eliminating the reactants and adding products. Therefore, I spent some time this week to edit the existing rules and adding the new rules asked by Thane and the equation based modeling group. Another important aspect that was discussed in the meeting was “DIVISION”. I have started to implement this function to our model. This function should get an environment as input and applies division to the environment and pass the new environment with double number of cells as its output. |
| - | I had also two other meetings this week. Lindsay meeting and iGEM meeting. | + | |
| | + | I had also two other meetings this week: a Lindsay meeting and an iGEM meeting. |
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| + | Miniprep B0015-R0040-luxOU-B0015 and NotI digest |
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| - | WIKI CODING HERE
| + | Overnights were miniprepped using Sigma GeneElute Miniprep Kit, eluting in 50uL ddH2O. Digest with ''Not''I (Invitrogen, CA) for 2h at 37oC. Reactions placed in freezer for Monday to run an agarose gel. |
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| | I will continue to expand o this and hopefully incorporate phosphatase treatment into the activity in the upcoming week. | | I will continue to expand o this and hopefully incorporate phosphatase treatment into the activity in the upcoming week. |
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| - | KEVIN
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| | As a side note, I talked to Max Chatnoir (from Genome Island) about her Eukaryotic cell so Stefan could generate some ideas on how to build and script the organelles of his cell he is designing. | | As a side note, I talked to Max Chatnoir (from Genome Island) about her Eukaryotic cell so Stefan could generate some ideas on how to build and script the organelles of his cell he is designing. |
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| + | In Lab, I helped to make Kan Plates. |
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CAROL
Preparation of Meeting
- Prepared for team meeting
- From the sequencing results of the forward and reverse reaction, the results did not confirm the sequence for luxCDABE. We decided to continue with biobrick cloning.
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CHINMOYEE
Looking into More Papers
- Stochastic Models of Gene Expression
- Stochastic mechanisms in gene expression
- A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways --- has stochastic rate constants
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EMILY
Ligation and Transformation of BBK LuxOD47E and the psB1AC3 Vector Take Two!
- Today there was no growth on the plates that I made yesterday, so I will have to re-ligate and transform as the Bacteria were not able to uptake the DNA for whatever reason.
- I followed ligation and transformationn protocols using the BBK LuxOD47E and the psB1AC3 vector that I digested previously. Once transformed, I plated this on C plates and left in the incubator for overnight growth.
- Today I also prepared for and partipated in our weekly team meeting, where each subgroup talked about their progress up to date, specifically what they accomplished this past week and what they plan to do next week.
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FAHD
Team presentations
Today we had our team presentations. I presented on behalf of the Human Practices aspect of our project.
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IMAN
Graphs, Rules, and First Steps in Division
Graph section of our model is completed this week. As it was mentioned, now we have two general types of graphs, one showing the change of concentration of an element in all the cells, and the other one shows the change of concentration of an element in each cell. There is a menu designed in result section that users can use to choose which one of these types of graphs they would like to observe.
This week, I also had a meeting with the other modeling team and we compared our models together. As a result of that meeting, we had to change and edit some of our evolution rules. Changing a rule in this model could not be done easily. When a rule changes, many functions should change too. For instance, some functions read rules and calculate the possibilities of their applications. Other functions apply the rules to the environment by eliminating the reactants and adding products. Therefore, I spent some time this week to edit the existing rules and adding the new rules asked by Thane and the equation based modeling group. Another important aspect that was discussed in the meeting was “DIVISION”. I have started to implement this function to our model. This function should get an environment as input and applies division to the environment and pass the new environment with double number of cells as its output.
I had also two other meetings this week: a Lindsay meeting and an iGEM meeting.
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JAMIE
Miniprep B0015-R0040-luxOU-B0015 and NotI digest
Overnights were miniprepped using Sigma GeneElute Miniprep Kit, eluting in 50uL ddH2O. Digest with NotI (Invitrogen, CA) for 2h at 37oC. Reactions placed in freezer for Monday to run an agarose gel.
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JEREMY
Constructing LuxPQ into psB1AC3 plasmid
Purpose: to insert linear LuxPQ into a BBK vector in order to continue the construction of signaling circuit with the BBK standard. Linear LuxPQ with BBK restriction sites was digested with the following sets of enzymes: XbaI and PstI, EcoRI and PstI. Using the same sets of enzymes, the psB1AC3 vector was also digested for 2 hours at 37ºC. Subsequent phosphotase and ligase treatment followed, as well as transformation into TOP10 competent cells. These cells were then plated on LB+ chlor plates overnight at 37ºC.
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KATIE
Putting Scripts into the Lab Equipment
I wrote out the pseudo code for the water bath script and the donor and recipient tubes for restriction digest this week as well as well as completing the first basic working version inside of test tubes instead of a basic primitive that were initially going to be given to the avatar so they could move and work with them anywhere they want, but know I believe that the tubes will remain in the lab and only be moved when they have to be sent to the water bath, heating block, etc. The order script is not complete yet, but that is because I am still changing it since other items will still have to be added to give something back to avatars.
Presently the test tubes will:
- Tell you if the item you added is correct or not. The tubes also tell you it is correct to delete something too, but hopefully other avatars will not have this permission. I will need to remove items that are not needed as well, which is where the cleaning script comes in as well as getting rid of items once they are no longer needed
- When touched, the tube will ask if you would like the circuit part to go behind or in front of another and then will search for specific enzymes depending on your choice and tells me if i can continue or not
I will continue to expand o this and hopefully incorporate phosphatase treatment into the activity in the upcoming week.
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MANDY
PCR and Gel Electrophoresis- Further Editing Second Life
PCR: the objects were renamed and rebuilt to match with what is required/produced during other experimental steps.
This was done after testing how the PCR and gel electrophoresis processes could be done together. Components for restriction digest (the first steps) were also built.
Did more testing on the Gel Electrophoresis activity: It is now "idiot proofed" to avoid wrong capitalization in user commands and out of order clicks. Notecards describing gel electrophoresis have been written.
As a side note, I talked to Max Chatnoir (from Genome Island) about her Eukaryotic cell so Stefan could generate some ideas on how to build and script the organelles of his cell he is designing.
In Lab, I helped to make Kan Plates.
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PRIMA
Continuation of Marketing
I shadowed Carol while she did restriction digest. She was doing construction. Her vector was apsB1AK3. However, since I didn't go into the lab very often, I wasn't sure what she was digesting. I just watched the processes and she just explained the restriction sites.
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STEFAN
Helping out in the lab
I've been finishing some objects that are going to be pit in the laboratory this week. Most notable are the microscope, various test tubes and scripted water bath. At the same time, arrangement adjustments we're carried out, creating walls for the labs, and an entry area as well as perfecting the Key Pad door I have been working on.
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VICKI
Colony PCR of J13002+LuxOD47A and LuxOD47A+B0015 bacteria
Purpose: Cultures grew successfully on plates last night. This will help confirm which of those colonies took up the plasmids that we wanted to, and that the plasmids that were taken up include properly-constructed genes in the right order.
Protocol: The colony PCR was conducted in accordance with that outlined on the protocol page. Platinum Taq polymerase was used, along with BBk construction primers. 5 colonies were tested for each construct, along with one negative control (for a total of 11 tubes being amplified).
Results: The gel is included below. The negative control results are peculiar, but are not raising any concern as the contamination band is not found anywhere else on the gel. Some of the LuxOD47A stock was run to serve as a size comparison. From this, it appears that the LuxOD47A+B0015 parts were successfully constructed and transformed, along with colonies 2 and 4 of the J13002+LuxOD47A parts.
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