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| | * Tried isolating a higher concentration of <i>luxCDABE</i> by using Qiagen Maxi-prep kit. | | * Tried isolating a higher concentration of <i>luxCDABE</i> by using Qiagen Maxi-prep kit. |
| | * I stopped at the precipitation of DNA step due to time constraints (Last step was elution in 15mL of Buffer QN) | | * I stopped at the precipitation of DNA step due to time constraints (Last step was elution in 15mL of Buffer QN) |
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| | Simbolic Math Tool : MuPad | | Simbolic Math Tool : MuPad |
| - | <br>Matlab's version of Maple . The MuPad interface in less daunting than the Matlab command line interface to do calculations . It solves Math problems such as limits , integrations , matricies etc . Can also plot data and graph equations . | + | <br>Matlab's version of Maple . The MuPad interface is less daunting than the Matlab command line interface to do calculations . It solves Math problems such as limits , integrations , matricies etc . Can also plot data and graph equations . |
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| | Statistical Toolbox : Distribution Fitting Tool , Polynomial Fitting Tool , Non-linear fitting Tool , Response surface modelling Tool , Analysis of Co-variance tool , Step wise regression tool , probability distribution function tool , Random Number Generation tool . | | Statistical Toolbox : Distribution Fitting Tool , Polynomial Fitting Tool , Non-linear fitting Tool , Response surface modelling Tool , Analysis of Co-variance tool , Step wise regression tool , probability distribution function tool , Random Number Generation tool . |
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| | Built AHL system in Simbiology. | | Built AHL system in Simbiology. |
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| | *Re-ran the PCR products from June 5th on a 1% agarose gel to see if we got better results for the negative control, indicating that there is no contamination. | | *Re-ran the PCR products from June 5th on a 1% agarose gel to see if we got better results for the negative control, indicating that there is no contamination. |
| - | Lanes 1-12 contain LuxOD47E template, Lane 13 is a negative control with ddH2O. See gel photo below.[[Image:Calgary_2009.06.10.LuxOD47E_Gradient_PCR.Tif]] | + | Lanes 1-12 contain LuxOD47E template, Lane 13 is a negative control with ddH2O. See gel photo below. |
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| | + | [[Image:2009.06.10.LuxOD47E_Gradient_PCR_(2).jpg|350px]] |
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| - | *There is still significant contamination in the negative control lane. We will re-do the entire PCR tp see if we can get a clean negative control lane. | + | *There is still significant contamination in the negative control lane. We will re-do the entire PCR to see if we can get a clean negative control lane. |
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| - | Looked into modelling deterministic and stochastic in symbiology. Stochastic modelling allows for predicting potential outcomes via variations in one or more inputs over time. On the other hand, the Deterministic model relies on mathmatical models to alter variables. | + | Looked into modelling deterministic and stochastic in Symbiology. Stochastic modelling allows for predicting potential outcomes via variations in one or more inputs over time. On the other hand, the Deterministic model relies on mathematical models to alter variables. |
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| | Integrated DNA technologies has generously offered to donate graph papers and sharpies. IDT is iGEM's community partner. | | Integrated DNA technologies has generously offered to donate graph papers and sharpies. IDT is iGEM's community partner. |
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CAROL
Plasmid Isolation of luxCDABE
- Tried isolating a higher concentration of luxCDABE by using Qiagen Maxi-prep kit.
- I stopped at the precipitation of DNA step due to time constraints (Last step was elution in 15mL of Buffer QN)
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CHINMOYEE
Exploring the reset of MatLab package
Simbolic Math Tool : MuPad
Matlab's version of Maple . The MuPad interface is less daunting than the Matlab command line interface to do calculations . It solves Math problems such as limits , integrations , matricies etc . Can also plot data and graph equations .
Statistical Toolbox : Distribution Fitting Tool , Polynomial Fitting Tool , Non-linear fitting Tool , Response surface modelling Tool , Analysis of Co-variance tool , Step wise regression tool , probability distribution function tool , Random Number Generation tool .
Built AHL system in Simbiology.
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EMILY
Gradient PCR Gel Electrophoresis Take Two
- Re-ran the PCR products from June 5th on a 1% agarose gel to see if we got better results for the negative control, indicating that there is no contamination.
Lanes 1-12 contain LuxOD47E template, Lane 13 is a negative control with ddH2O. See gel photo below.
- There is still significant contamination in the negative control lane. We will re-do the entire PCR to see if we can get a clean negative control lane.
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JAMIE
Construction of luxOU into psB1AC3
Gradient PCR products were pooled and purified using the QIAquick PCR Purification kit (Qiagen, MD). Restriction digest of vector and insert were set up using both XbaI with PstI and EcoRI with PstI (Invitrogen, CA) according to manufacturer's instructions. Digest for 2h at 37oC. Followed with Antarctic Phosphatase (New England Biolabs, ON) treatment (standard manufacturer instructions) for 30minutes at room temperature and heat deactivation at 65oC. QuikLigase (New England Biolabs, ON) ligated 5uL of both insert and vector (standard manufacturer instructions). Ligation products were transformed into TOP10 competent cells with heat shock at 37oC for 5 minutes (for protocol see Sambrook et al., 2001).
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JEREMY
Sequencing results of luxPQ and next steps
DNA sequencing results came back for luxPQ C24-1, revealing the presence of luxPQ in the TOPO vector. The next step will be to biobrick clone this piece into psB1AK3 by doing a gradient PCR.
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KEVIN
Matlab and Symbiology
Looked into modelling deterministic and stochastic in Symbiology. Stochastic modelling allows for predicting potential outcomes via variations in one or more inputs over time. On the other hand, the Deterministic model relies on mathematical models to alter variables.
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PRIMA
Continuation with Marketing
I made a few cold calls today.
Company 1 - not available- follow up tomorrow
Company 2 - called, needs more time to think proposal over
Company 4 - called but not available, left a message, follow up tomorrow
Compnay 5+6 - called but not available, left a voicemail, follow up later this week. I also sent them a follow up email.
Integrated DNA technologies has generously offered to donate graph papers and sharpies. IDT is iGEM's community partner.
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VICKI
Re-do of gradient PCR gel because of contamination issues
Purpose: We considered the possibility that lanes might have been mixed up from the June 4 gradient PCR. Today, we ran the PCR product on a gel with greater care and attention.
Materials and methods:
Volumes: 3 uL PCR product, 2 uL dye, 15 uL ddHOH. Load 17 uL into the wells and run at 120 V for 40 min.
Results: As ugly as the last. We will definitely re-do the gradient PCR.
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