IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-10: Difference between revisions

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<div class="tabs">
{{IGEM:/Harvard/2006/Cyanobacteria}}
<ul>
<li>[[IGEM:Harvard/2006/Cyanobacteria|1. Main Page]]</li>
<li id="current">[[IGEM:Harvard/2006/Cyanobacteria/Notebook|2. Lab Notebook]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Literature|3. Literature]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Incubator|4. Incubator]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Protocols|5. Protocols]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Care|6. Care]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Contacts|7. Contacts]]</li>
</ul>
</div>
<br style="clear:both">
<div class="tabcontent">


<div class="tabs">
<div class="tabs">
<ul>
<ul>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-7 | Previous Entry]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-7 | Previous Entry]]</li>
<li id="current">[[IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-10 | Current Entry]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-10 | Current Entry]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-11 | Next Entry]]</li>
<li>[[IGEM:Harvard/2006/Cyanobacteria/Notebook/2006-7-11 | Next Entry]]</li>
</ul>
</ul>
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| align="center" style="background:#f0f0f0;"|'''PCR MACHINE'''
| align="center" style="background:#f0f0f0;"|'''PCR MACHINE'''
| align="center" style="background:#f0f0f0;"|'''REACTION'''
| align="center" style="background:#f0f0f0;"|'''REACTION'''
| align="center" style="background:#f0f0f0;"|'''PWNED BY'''
|-
|-
| 1||Cy7942||Cy primers||Old Taq||-||Old NTPs||65\'||1
| 1||Cy7942||Cy primers||Old Taq||-||Old NTPs||65\'||1||D||Peng
|-
|-
| 2||Cy7942||Cy primers||New Taq||2mM||Old NTPs||65\'||1||A
| 2||Cy7942||Cy primers||New Taq||2mM||Old NTPs||65\'||1||A||Hetmann
|-
|-
| 3||Cy7942||Cy primers||Old Taq||-||New NTPs||65\'||1
| 3||Cy7942||Cy primers||Old Taq||-||New NTPs||65\'||1||D||Peng
|-
|-
| 4||Cy7942||Cy primers||New Taq||2mM||New NTPs||65\'||1||A
| 4||Cy7942||Cy primers||New Taq||2mM||New NTPs||65\'||1||A||Hetmann
|-
|-
| 5||Cy7942||Cy primers||New Taq||4mM||New NTPs||65\'||1||B
| 5||Cy7942||Cy primers||New Taq||4mM||New NTPs||65\'||1||B||Dave
|-
|-
| 6||Cy7942||Cy primers||New Taq||6mM||New NTPs||65\'||1||C
| 6||Cy7942||Cy primers||New Taq||6mM||New NTPs||65\'||1||C||Jeff
|-
|-
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
|-
|-
| 7||Biobrick Miniprep||Biobrick Primer||Old Taq||-||Old NTPs||65\'||1
| 7||Biobrick Miniprep||Biobrick Primer||Old Taq||-||Old NTPs||65\'||1||E||Peng
|-
|-
| 8||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||Old NTPs||65\'||1||A
| 8||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||Old NTPs||65\'||1||A||Hetmann
|-
|-
| 9||Biobrick Miniprep||Biobrick Primer||Old Taq||-||New NTPs||65\'||1
| 9||Biobrick Miniprep||Biobrick Primer||Old Taq||-||New NTPs||65\'||1||E||Peng
|-
|-
| 10||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||65\'||1||A
| 10||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||65\'||1||A||Hetmann
|-
|-
| 11||Biobrick Miniprep||Biobrick Primer||New Taq||4mM||New NTPs||65\'||1||B
| 11||Biobrick Miniprep||Biobrick Primer||New Taq||4mM||New NTPs||65\'||1||B||Dave
|-
|-
| 12||Biobrick Miniprep||Biobrick Primer||New Taq||6mM||New NTPs||65\'||1||C
| 12||Biobrick Miniprep||Biobrick Primer||New Taq||6mM||New NTPs||65\'||1||C||Jeff
|-
|-
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
|-
|-
| 13||Cy7942||Cy primers||New Taq||2mM||New NTPs||55\'||1||A
| 13||Cy7942||Cy primers||New Taq||2mM||New NTPs||55\'||2||A||Hetmann
|-
|-
| 14||Cy7942||Cy primers||New Taq||4mM||New NTPs||55\'||1||B
| 14||Cy7942||Cy primers||New Taq||4mM||New NTPs||55\'||2||B||Dave
|-
|-
| 15||Cy7942||Cy primers||New Taq||6mM||New NTPs||55\'||1||C
| 15||Cy7942||Cy primers||New Taq||6mM||New NTPs||55\'||2||C||Jeff
|-
|-
| 16||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||55\'||1||A
| 16||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||55\'||2||A||Hetmann
|-
|-
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
|-
|-
| 17||Cy7942||Cy primers||New Taq||2mM||New NTPs||65\'||2||A
| 17||Cy7942||Cy primers||New Taq||2mM||New NTPs||65\'||1||A||Hetmann
|-
|-
| 18||Cy7942||Cy primers||New Taq||4mM||New NTPs||65\'||2||B
| 18||Cy7942||Cy primers||New Taq||4mM||New NTPs||65\'||1||B||Dave
|-
|-
| 19||Cy7942||Cy primers||New Taq||6mM||New NTPs||65\'||2||C
| 19||Cy7942||Cy primers||New Taq||6mM||New NTPs||65\'||1||C||Jeff
|-
|-
| 20||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||65\'||2||A
| 20||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||65\'||1||A||Hetmann
|-
|-
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
| &nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;||&nbsp;
|-
|-
| 21||Cy7942||Cy primers||New Taq||2mM||New NTPs||55\'||2||A
| 21||Cy7942||Cy primers||New Taq||2mM||New NTPs||55\'||2||A||Hetmann
|-
|-
| 22||Cy7942||Cy primers||New Taq||4mM||New NTPs||55\'||2||B
| 22||Cy7942||Cy primers||New Taq||4mM||New NTPs||55\'||2||B||Dave
|-
|-
| 23||Cy7942||Cy primers||New Taq||6mM||New NTPs||55\'||2||C
| 23||Cy7942||Cy primers||New Taq||6mM||New NTPs||55\'||2||C||Jeff
|-
|-
| 24||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||55\'||2||A
| 24||Biobrick Miniprep||Biobrick Primer||New Taq||2mM||New NTPs||55\'||2||A||Hetmann
|-
|-
|  
|  
Line 127: Line 116:
| align="center" style="background:#f0f0f0;"|'''REACTION B'''
| align="center" style="background:#f0f0f0;"|'''REACTION B'''
| align="center" style="background:#f0f0f0;"|'''REACTION C'''
| align="center" style="background:#f0f0f0;"|'''REACTION C'''
| align="center" style="background:#f0f0f0;"|'''REACTION D'''
| align="center" style="background:#f0f0f0;"|'''REACTION E'''
|-
|-
| 2 mM [Mg] || 4 mM [Mg] || 6 mM [Mg]  
| 2 mM [Mg] || 4 mM [Mg] || 6 mM [Mg]  
|-
|-
| 10 μL template || 10 μL template || 10 μL template  
| 10 μL template || 10 μL template || 10 μL template || 5uL template || 1 uL template
|-
|-
| 10 μL 10x buffer || 10 μL 10x buffer || 10 μL 10x buffer
| 10 μL 10x buffer || 10 μL 10x buffer || 10 μL 10x buffer || 5 uL 10x buffer || 5 uL 10x buffer
|-
|-
| 2 μL dNTP || 2 μL dNTP || 2 μL dNTP
| 2 μL 10 mM dNTP || 2 μL 10 mM dNTP || 2 μL 10 mM dNTP || 1 uL 10mM dNTP
|-
|-
| 2 μL Primer 1 || 2 μL Primer 1 || 2 μL Primer 1  
| 2 μL Primer 1 || 2 μL Primer 1 || 2 μL Primer 1 || 1 uL Primer 1 || 1 uL Primer 2
|-
|-
| 2 μL Primer 2 || 2 μL Primer 2 || 2 μL Primer 2  
| 2 μL Primer 2 || 2 μL Primer 2 || 2 μL Primer 2 || 1 uL Primer 2 || 1 uL Primer 2
|-
|-
| 1 μL Taq || 1 μL Taq || 1 μL Taq
| 1 μL Taq || 1 μL Taq || 1 μL Taq || 0.5 uL Taq || 0.5 uL Taq
|-
|-
| 73 μL dH<sub>2</sub>0 || 71 μL dH<sub>2</sub>0 || 69 μL dH<sub>2</sub>0
| 73 μL dH<sub>2</sub>0 || 71 μL dH<sub>2</sub>0 || 69 μL dH<sub>2</sub>0 || 37 μL dH<sub>2</sub>0 || 41 μL dH<sub>2</sub>0  
|-
|-
| - || 2 μL 100 mM Mg || 4 μL 100 mM Mg
| - || 2 μL 100 mM Mg || 4 μL 100 mM Mg
|  
|  
|}
|}
==Notes==
1) Some were made with 10uL positive control instead of 2uL; may affect results (Jeff and Dave's samples)
2) The Run tims is:
PCR5: @ 55C anneal:
  #94C, 15'
  #94C, 30"
  #56C, 30"
  #72C, 3.5'
  #Cycle to step 2, 7x
  #94C, 30"
  #55C, 30"
  #72C, 3.5'
  #Cycle to step 6, 30x
  #72C, 5'
  #4C hold
PCR6: @ 65C anneal:
  #94C, 15'
  #94C, 30"
  #56C, 30"
  #72C, 3.5'
  #Cycle to step 2, 7x
  #94C, 30"
  #65C, 30"
  #72C, 3.5'
  #Cycle to step 6, 30x
  #72C, 5'
  #4C hold

Latest revision as of 09:05, 10 August 2006

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Newer entries at the bottom.

Oscillation model

Jeff finished adding sinusoidal and feedback alpha functions to his model. He will upload the code later.

Meeting

We had our weekly team meeting today. Several people made some good points and suggestions:

  • For solution #2, we can simply wash the exogenous chemical away (e.g. lactose) to disable expression at will. Pam expressed reservations about the heat shock in solution #1. We can substitute solution #2 for solution #1 by washing. In other words, we can fulfill both experiments of interest-- constant KaiABC production and initial KaiABC production-- with just one promoter.
  • As Nick pointed out in an earlier email, even if we can't see oscillation, we can still at least show that something is happening. KaiC stays unphosphorylated in the absence of KaiA and KaiB. If we notice that KaiC is, say, 50% phosphorylated, then, even if we can't observe oscillation, we know KaiABC are interacting.
  • Pam suggested that we synthesize our KaiABC BB constructs in parallel with PCRing out of PCC 7942, to cover our bases in case the PCR takes a long time.
  • Regarding PCR, William pointed out that we might obtain a higher yield by lysing our cells chemically instead of relying on temperature.
  • Also, we should do more research on PCR protocols for cyanobacteria.
  • In the future, we should organize our presentations a little better and give a high-level overview at the start.

New cultures of PCC 7942

Our new culture grew quickly

Both flasks from Friday showed growth. The flask with thiosulfate was rich green while the flask without was paler. We were surprised and pleased to find that our cyanobacteria was growing so quickly.

DNA Synthesis companies

  1. Blue Heron Biotechnology, Inc.
    • Advertised as 2-4 weeks, but teams have had problems getting sequences on time in the past.
  2. Codon Devices, Inc.
  3. DNA 2.0, Inc.

Add more links here. Additional information would be useful.

Frozen stocks

Peng made frozen stocks of our newly grown PCC 7942. (Peng fill this in)

Mega PCR Debug

LABEL SUBSTRATE PRIMERS TAQ + ATP [Mg+] NTP ANNEALING TEMP PCR MACHINE REACTION PWNED BY
1 Cy7942 Cy primers Old Taq - Old NTPs 65\' 1 D Peng
2 Cy7942 Cy primers New Taq 2mM Old NTPs 65\' 1 A Hetmann
3 Cy7942 Cy primers Old Taq - New NTPs 65\' 1 D Peng
4 Cy7942 Cy primers New Taq 2mM New NTPs 65\' 1 A Hetmann
5 Cy7942 Cy primers New Taq 4mM New NTPs 65\' 1 B Dave
6 Cy7942 Cy primers New Taq 6mM New NTPs 65\' 1 C Jeff
               
7 Biobrick Miniprep Biobrick Primer Old Taq - Old NTPs 65\' 1 E Peng
8 Biobrick Miniprep Biobrick Primer New Taq 2mM Old NTPs 65\' 1 A Hetmann
9 Biobrick Miniprep Biobrick Primer Old Taq - New NTPs 65\' 1 E Peng
10 Biobrick Miniprep Biobrick Primer New Taq 2mM New NTPs 65\' 1 A Hetmann
11 Biobrick Miniprep Biobrick Primer New Taq 4mM New NTPs 65\' 1 B Dave
12 Biobrick Miniprep Biobrick Primer New Taq 6mM New NTPs 65\' 1 C Jeff
               
13 Cy7942 Cy primers New Taq 2mM New NTPs 55\' 2 A Hetmann
14 Cy7942 Cy primers New Taq 4mM New NTPs 55\' 2 B Dave
15 Cy7942 Cy primers New Taq 6mM New NTPs 55\' 2 C Jeff
16 Biobrick Miniprep Biobrick Primer New Taq 2mM New NTPs 55\' 2 A Hetmann
               
17 Cy7942 Cy primers New Taq 2mM New NTPs 65\' 1 A Hetmann
18 Cy7942 Cy primers New Taq 4mM New NTPs 65\' 1 B Dave
19 Cy7942 Cy primers New Taq 6mM New NTPs 65\' 1 C Jeff
20 Biobrick Miniprep Biobrick Primer New Taq 2mM New NTPs 65\' 1 A Hetmann
               
21 Cy7942 Cy primers New Taq 2mM New NTPs 55\' 2 A Hetmann
22 Cy7942 Cy primers New Taq 4mM New NTPs 55\' 2 B Dave
23 Cy7942 Cy primers New Taq 6mM New NTPs 55\' 2 C Jeff
24 Biobrick Miniprep Biobrick Primer New Taq 2mM New NTPs 55\' 2 A Hetmann

PCR Reactions

REACTION A REACTION B REACTION C REACTION D REACTION E
2 mM [Mg] 4 mM [Mg] 6 mM [Mg]
10 μL template 10 μL template 10 μL template 5uL template 1 uL template
10 μL 10x buffer 10 μL 10x buffer 10 μL 10x buffer 5 uL 10x buffer 5 uL 10x buffer
2 μL 10 mM dNTP 2 μL 10 mM dNTP 2 μL 10 mM dNTP 1 uL 10mM dNTP
2 μL Primer 1 2 μL Primer 1 2 μL Primer 1 1 uL Primer 1 1 uL Primer 2
2 μL Primer 2 2 μL Primer 2 2 μL Primer 2 1 uL Primer 2 1 uL Primer 2
1 μL Taq 1 μL Taq 1 μL Taq 0.5 uL Taq 0.5 uL Taq
73 μL dH20 71 μL dH20 69 μL dH20 37 μL dH20 41 μL dH20
- 2 μL 100 mM Mg 4 μL 100 mM Mg

Notes

1) Some were made with 10uL positive control instead of 2uL; may affect results (Jeff and Dave's samples)

2) The Run tims is:

PCR5: @ 55C anneal: 

 #94C, 15'
 #94C, 30"
 #56C, 30"
 #72C, 3.5'
 #Cycle to step 2, 7x
 #94C, 30"
 #55C, 30"
 #72C, 3.5'
 #Cycle to step 6, 30x
 #72C, 5'
 #4C hold

PCR6: @ 65C anneal: 

 #94C, 15'
 #94C, 30"
 #56C, 30"
 #72C, 3.5'
 #Cycle to step 2, 7x
 #94C, 30"
 #65C, 30"
 #72C, 3.5'
 #Cycle to step 6, 30x
 #72C, 5'
 #4C hold
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