Team:Calgary/16 July 2009

From 2009.igem.org

(Difference between revisions)
Line 484: Line 484:
<br>
<br>
<div class="heading">
<div class="heading">
-
Descriptive Title of What You're Doing
+
Movement and Modification
</div>
</div>
<br>
<br>
<div class="desc">
<div class="desc">
</html>
</html>
-
WIKI CODING HERE
+
The gel electrophoresis script has been modified and now it should be simple for Mandy to add any conditionals she would like to suit the lab activities. Also, the tube for bacteria transformation now has another tube beside it and every time a question for the quiz is answered, the tube will fill up a little more and once it reaches the top it will reset for another person to take the quiz. I would like to change the colours each time a question is answered depending on whether it was answered correctly or not, but for now it fills up using a green colour.
 +
<br>
 +
<br>
 +
The water bath script is now being modified and I am inserting movement scripts using llSetPos() function into the donor and recipient tubes for restriction digest (due to my horrible attentiveness to saving, I lost this once today when second life froze my laptop – luckily the script is not too long). It is all under comments for now in the recipient tube and the donor tube is undergoing testing with the current script. The water bath listen script has been set up and the top will open using the touch_start event at the moment, which I will transfer to listen so that when the test tube begins to move over to it the top will open. 
 +
<br>
 +
<br>
 +
Once again the restriction digest tubes cannot be used the way they were intended while I add the movement code to the existing script so this activity will probably be under construction until early next week. I will still need to determine the proper placement for the tubes as they move so they do not go through the walls of the water bath, actually end up in the water and do not end up in the exact same place to appear as one tube.
 +
<br>
 +
<br>
 +
Tomorrow I would like to:
 +
* Finish up the listen/response scripts that I started for the heating block and phosphatase treatment that were adapted from the water bath.
 +
* Get the movement of the tubes for restriction digest moving smoothly and to the proper positions within the lab. If I am able to complete this I believe I will clean up a couple of my scripts so that they look presentable for the video I have to do for the blog next Tuesday.
 +
* If I am able to get restriction digest functioning again, I would like to return to working on the sequencer, which I have neglected this week. I will need to test the note card reading script to make sure it is functioning the way I would like it to and then I will add it to the sequencer.
 +
 
<html>
<html>

Revision as of 20:43, 17 August 2009

University of Calgary

UNIVERSITY OF CALGARY



THIS MONTH

July
MTWTFSS
    1 2 3 4 5
6 7 8 9 10 11 12
13 14 15 16 17 18 19
20 21 22 23 24 25 26
27 28 29 30 31


NOTEBOOK PAGE INDEX



CALENDAR

May
MTWTFSS
        1 2 3
4 5 6 7 8 9 10
11 12 13 14 15 16 17
18 19 20 21 22 23 24
25 26 27 28 29 30 31


June
MTWTFSS
1 2 3 4 5 6 7
8 9 10 11 12 13 14
15 16 17 18 19 20 21
22 23 24 25 26 27 28
29 30


July
MTWTFSS
    1 2 3 4 5
6 7 8 9 10 11 12
13 14 15 16 17 18 19
20 21 22 23 24 25 26
27 28 29 30 31


August
MTWTFSS
          1 2
3 4 5 6 7 8 9
10 11 12 13 14 15 16
17 18 19 20 21 22 23
24 25 26 27 28 29 30
31


September
MTWTFSS
  1 2 3 4 5 6
7 8 9 10 11 12 13
14 15 16 17 18 19 20
21 22 23 24 25 26 27
28 29 30


October
MTWTFSS
      1 2 3 4
5 6 7 8 9 10 11
12 13 14 15 16 17 18
19 20 21 22 23 24 25
26 27 28 29 30 31



JULY 16, 2009


CAROL

Diluting Primers and Primer Extension Polymerase Chain Reaction (PCR)

  • To create the synthetic sigma 70 promoter library, we have synthesized 32 different primers (16 different forward primers and 16 different reverse primers) to hopefully form 256 different promoters.
  • Need to dilute primers to 80μM. The following is the concentration of the original primers that were synthesized once water was added to the primers.
Primer 260/280 260/230 Concentration [ng/μL] Reading/2.5 [ng/μL] Stock Concentration [μM] Volume stock into working [μL] Volume water into working [μL]
sig70-F1 1.98 1.73 20816 832.64 60.07 6.7 43.3
sig70-F2 1.55 1.80 44284 17713.6 1277.91 3.1 46.9
sig70-F3 1.62 1.86 4132316529.21192.463.446.6
sig70-F4 1.70 1.99 3236512946933.964.345.7
sig70-F5 1.72 2.07 3368813475.2972.144.145.9
sig70-F6 2.07 1.954541218164.81310.463.146.9
sig70-F7 1.64 1.95 3904615618.41126.763.646.4
sig70-F8 1.43 1.63 45745182981320.073.047.0
sig70-F9 1.75 2.16 236289451.2681.845.944.1
sig70-F10 1.72 2.013268213072.8943.114.245.8
sig70-F11 1.71 2.073149412597.6908.834.445.6
sig70-F12 1.59 1.82 4120216480.81188.973.446.6
sig70-F13 1.73 2.03 2922411689.6843.34.745.3
sig70-F14 1.411.58 45645182581317.23.047.0
sig70-F15 1.59 1.85 4068116272.41173.93.446.6
sig70-F16 1.57 1.82 4224116896.41219.03.346.7
sig70-R1 2.06 2.17 75163006.4216.918.431.6
sig70-R2 2.04 2.25 152556102.0440.29.140.9
sig70-R3 1.76 1.85 4250317001.21226.53.346.7
sig70-R42.012.21240129604.8692.95.844.2
sig70-R52.102.27185307412534.77.542.5
sig70-R61.982.192845211380.8821.04.945.1
sig70-R7 1.942.173297613190.4951.64.245.8
sig70-R8 2.002.202537910151.6732.45.544.5
sig70-R9 2.00 2.24 241419656.4696.65.944.1
sig70-R10 1.94 2.17 3023712094.8872.64.645.4
sig70-R11 1.922.16 3149712598.8908.94.445.6
sig70-R12 1.92 2.17 3004512018867.04.645.4
sig70-R13 2.012.18187267490.4540.47.442.6
sig70-R14 1.88 2.033611114444.41042.13.846.2
sig70-R15 1.98 2.17106794271.6308.21337
sig70-R16 1.86 2.01 3596914387.610383.946.1
  • The sequences for each primer is listed in the following table:


Primer Sequence
sig70-F1 GCGCGCTCGAGAATAATTCTTAAAATTTATGCTTCCGGCTCG
sig70-F2 GCGCGCTCGAGAATAATTCTTAATATTTATGCTTCCGGCTCG
sig70-F3 GCGCGCTCGAGAATAATTCTTAAGATTTATGCTTCCGGCTCG
sig70-F4 GCGCGCTCGAGAATAATTCTTAACATTTATGCTTCCGGCTCG
sig70-F5 GCGCGCTCGAGAATAATTCTTTAAATTTATGCTTCCGGCTCG
sig70-F6 GCGCGCTCGAGAATAATTCTTTATATTTATGCTTCCGGCTCG
sig70-F7 GCGCGCTCGAGAATAATTCTTTAGATTTATGCTTCCGGCTCG
sig70-F8 GCGCGCTCGAGAATAATTCTTTACATTTATGCTTCCGGCTCG
sig70-F9 GCGCGCTCGAGAATAATTCTTGAAATTTATGCTTCCGGCTCG
sig70-F10 GCGCGCTCGAGAATAATTCTTGATATTTATGCTTCCGGCTCG
sig70-F11 GCGCGCTCGAGAATAATTCTTGAGATTTATGCTTCCGGCTCG
sig70-F12 GCGCGCTCGAGAATAATTCTTGACATTTATGCTTCCGGCTCG
sig70-F13 GCGCGCTCGAGAATAATTCTTCAAATTTATGCTTCCGGCTCG
sig70-F14 GCGCGCTCGAGAATAATTCTTCATATTTATGCTTCCGGCTCG
sig70-F15 GCGCGCTCGAGAATAATTCTTCAGATTTATGCTTCCGGCTCG
sig70-F16 GCGCGCTCGAGAATAATTCTTCACATTTATGCTTCCGGCTCG
sig70-R1 GCGGGATCCAATTGCACGTAAAATACGAGCCGGAAGCATAAA
sig70-R2 GCGGGATCCAATTGCACGTAATATACGAGCCGGAAGCATAAA
sig70-R3 GCGGGATCCAATTGCACGTAACATACGAGCCGGAAGCATAAA
sig70-R4GCGGGATCCAATTGCACGTAAGATACGAGCCGGAAGCATAAA
sig70-R5GCGGGATCCAATTGCACGTATAATACGAGCCGGAAGCATAAA
sig70-R6GCGGGATCCAATTGCACGTATTATACGAGCCGGAAGCATAAA
sig70-R7 GCGGGATCCAATTGCACGTATGATACGAGCCGGAAGCATAAA
sig70-R8 GCGGGATCCAATTGCACGTATCATACGAGCCGGAAGCATAAA
sig70-R9 GCGGGATCCAATTGCACGTAGAATACGAGCCGGAAGCATAAA
sig70-R10 GCGGGATCCAATTGCACGTAGTATACGAGCCGGAAGCATAAA
sig70-R11 GCGGGATCCAATTGCACGTAGGATACGAGCCGGAAGCATAAA
sig70-R12 GCGGGATCCAATTGCACGTAGCATACGAGCCGGAAGCATAAA
sig70-R13 GCGGGATCCAATTGCACGTACAATACGAGCCGGAAGCATAAA
sig70-R14 GCGGGATCCAATTGCACGTACTATACGAGCCGGAAGCATAAA
sig70-R15 GCGGGATCCAATTGCACGTACGATACGAGCCGGAAGCATAAA
sig70-R16 GCGGGATCCAATTGCACGTACCATACGAGCCGGAAGCATAAA
  • Stock dATP, dGTP, dCTP, dTTP from Invitrogen was diluted from 100mM to 0.5mM.
  • See how the primer extension PCR is done in the protocol page.
  • Both the varying promoters and the vector, pCS26, was digested using enzymes, XhoI and BamHI overnight. The vector was incubated at 37oC and the promoter was digested for 2 hours at 16oC and then overnight at room temperature (~21oC).


CHINMOYEE

Descriptive Title of What You're Doing

WIKI CODING HERE


EMILY

Descriptive Title of What You're Doing

WIKI CODING HERE


FAHD

Descriptive Title of What You're Doing

WIKI CODING HERE


IMAN

Descriptive Title of What You're Doing

WIKI CODING HERE


JAMIE

Descriptive Title of What You're Doing

WIKI CODING HERE


JEREMY

Descriptive Title of What You're Doing

WIKI CODING HERE


KATIE

Movement and Modification

The gel electrophoresis script has been modified and now it should be simple for Mandy to add any conditionals she would like to suit the lab activities. Also, the tube for bacteria transformation now has another tube beside it and every time a question for the quiz is answered, the tube will fill up a little more and once it reaches the top it will reset for another person to take the quiz. I would like to change the colours each time a question is answered depending on whether it was answered correctly or not, but for now it fills up using a green colour.

The water bath script is now being modified and I am inserting movement scripts using llSetPos() function into the donor and recipient tubes for restriction digest (due to my horrible attentiveness to saving, I lost this once today when second life froze my laptop – luckily the script is not too long). It is all under comments for now in the recipient tube and the donor tube is undergoing testing with the current script. The water bath listen script has been set up and the top will open using the touch_start event at the moment, which I will transfer to listen so that when the test tube begins to move over to it the top will open.

Once again the restriction digest tubes cannot be used the way they were intended while I add the movement code to the existing script so this activity will probably be under construction until early next week. I will still need to determine the proper placement for the tubes as they move so they do not go through the walls of the water bath, actually end up in the water and do not end up in the exact same place to appear as one tube.

Tomorrow I would like to:

  • Finish up the listen/response scripts that I started for the heating block and phosphatase treatment that were adapted from the water bath.
  • Get the movement of the tubes for restriction digest moving smoothly and to the proper positions within the lab. If I am able to complete this I believe I will clean up a couple of my scripts so that they look presentable for the video I have to do for the blog next Tuesday.
  • If I am able to get restriction digest functioning again, I would like to return to working on the sequencer, which I have neglected this week. I will need to test the note card reading script to make sure it is functioning the way I would like it to and then I will add it to the sequencer.



KEVIN

Descriptive of What You're Doing

WIKI CODING HERE


MANDY

Descriptive Title of What You're Doing

WIKI CODING HERE


PATRICK

Descriptive Title of What You're Doing

WIKI CODING HERE


PRIMA

Descriptive Title of What You're Doing

WIKI CODING HERE


STEFAN

Descriptive Title of What You're Doing

WIKI CODING HERE


VICKI

Descriptive Title of What You're Doing

WIKI CODING HERE