Team:KULeuven/29 August 2008

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== Lab Work ==
== Lab Work ==
=== Wet Lab ===
=== Wet Lab ===
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* A liquid culture was made of the new parts and the ligations we did. We will Miniprep them tomorrow.
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A liquid culture was made of the new parts and the ligations we did. We will miniprep them tomorrow.
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* We also did a colony PCR to test yesterday's ligations. They don't seem to be correct.
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* Some more digests were made and purified out of gel: <div style="margin-left:10px;"> cut with ''Xba''I and ''Eco''RI -> B0032. </div> <div style="margin-left:10px;"> cut with ''Xba''I and ''Pst''I -> B0015. </div> <div style="margin-left:10px;"> cut with ''Spe''I and ''Pst''I -> C0012, C0040, C0060, K145015, K145001 and K145151. </div>
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We also did a colony PCR to test yesterday's ligations. They don't seem to be correct. Well, the PCR failed - we couln't see anything on the gel (probably not enough template).
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* Ligations were set up: R0011+B0032, (R0040+J23922)+(J23109+J23032), C0012+B0015, C0060+B0015, C0040+B0015, K145015+B0015, K145001+B0015 and K145151+B0015.
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Some more digests were made and purified out of gel:  
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** cut with ''Xba''I and ''Eco''RI -> [http://partsregistry.org/Part:BBa_B0032 B0032].
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** cut with ''Xba''I and ''Pst''I -> [http://partsregistry.org/Part:BBa_B0015 B0015].
 +
** cut with ''Spe''I and ''Pst''I -> [http://partsregistry.org/Part:BBa_C0012 C0012], [http://partsregistry.org/Part:BBa_C0040 C0040], [http://partsregistry.org/Part:BBa_C0060 C0060], [http://partsregistry.org/Part:BBa_K145015 K145015], [http://partsregistry.org/Part:BBa_K145001 K145001] and [http://partsregistry.org/Part:BBa_K145151 K145151].
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Ligations were set up: [http://partsregistry.org/Part:BBa_R0011 R0011]+[http://partsregistry.org/Part:BBa_B0032 B0032], ([http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_J23022 J23022])+([http://partsregistry.org/Part:BBa_J23109 J23109]+[http://partsregistry.org/Part:BBa_J23032 J23032]), [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0060 C0060]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0012 C0012]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145015 K145015]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145001 K145001]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145151 K145151]+[http://partsregistry.org/Part:BBa_B0015 B0015].
=== Dry Lab ===
=== Dry Lab ===
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==== Meeting ====
Had another good meeting today. Possibility was raised that adenosine methylation by the dam methylase is inhibiting our XbaI GATC restrictions. Checking it out. JM109 is probably dam+ so XbaI shouldn't cut, while for example JM110 and DM1 (Invitrogen) are dam-. If we want to use XbaI we'll need dam- cells.
Had another good meeting today. Possibility was raised that adenosine methylation by the dam methylase is inhibiting our XbaI GATC restrictions. Checking it out. JM109 is probably dam+ so XbaI shouldn't cut, while for example JM110 and DM1 (Invitrogen) are dam-. If we want to use XbaI we'll need dam- cells.
'''Edit: ''Dam methylation seems not to be responsible for the failure of BBa_B0015. Probably the big issue is the vector around BBa_B0015 which causes troubles.'' See [http://partsregistry.org/Part:BBa_B0015:Experience this] page.'''
'''Edit: ''Dam methylation seems not to be responsible for the failure of BBa_B0015. Probably the big issue is the vector around BBa_B0015 which causes troubles.'' See [http://partsregistry.org/Part:BBa_B0015:Experience this] page.'''
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==== Ethics ====
Ethics, bioethics and more ethics.
Ethics, bioethics and more ethics.
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==== Wiki ====
==== Wiki ====
All parameters on the wiki AND in the MatLab model have been checked and should be correct.
All parameters on the wiki AND in the MatLab model have been checked and should be correct.
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== Remarks ==
 
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{{:Team:KULeuven/Tools/New_Day/Date_Retriever}}
 

Latest revision as of 15:06, 12 October 2008

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< previous friday ← yesterday tomorrow → next monday >

Contents

Lab Work

Wet Lab

A liquid culture was made of the new parts and the ligations we did. We will miniprep them tomorrow.

We also did a colony PCR to test yesterday's ligations. They don't seem to be correct. Well, the PCR failed - we couln't see anything on the gel (probably not enough template).

Some more digests were made and purified out of gel:

    • cut with XbaI and EcoRI -> [http://partsregistry.org/Part:BBa_B0032 B0032].
    • cut with XbaI and PstI -> [http://partsregistry.org/Part:BBa_B0015 B0015].
    • cut with SpeI and PstI -> [http://partsregistry.org/Part:BBa_C0012 C0012], [http://partsregistry.org/Part:BBa_C0040 C0040], [http://partsregistry.org/Part:BBa_C0060 C0060], [http://partsregistry.org/Part:BBa_K145015 K145015], [http://partsregistry.org/Part:BBa_K145001 K145001] and [http://partsregistry.org/Part:BBa_K145151 K145151].

Ligations were set up: [http://partsregistry.org/Part:BBa_R0011 R0011]+[http://partsregistry.org/Part:BBa_B0032 B0032], ([http://partsregistry.org/Part:BBa_R0040 R0040]+[http://partsregistry.org/Part:BBa_J23022 J23022])+([http://partsregistry.org/Part:BBa_J23109 J23109]+[http://partsregistry.org/Part:BBa_J23032 J23032]), [http://partsregistry.org/Part:BBa_C0040 C0040]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0060 C0060]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0012 C0012]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145015 K145015]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145001 K145001]+[http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_K145151 K145151]+[http://partsregistry.org/Part:BBa_B0015 B0015].

Dry Lab

Meeting

Had another good meeting today. Possibility was raised that adenosine methylation by the dam methylase is inhibiting our XbaI GATC restrictions. Checking it out. JM109 is probably dam+ so XbaI shouldn't cut, while for example JM110 and DM1 (Invitrogen) are dam-. If we want to use XbaI we'll need dam- cells.

Edit: Dam methylation seems not to be responsible for the failure of BBa_B0015. Probably the big issue is the vector around BBa_B0015 which causes troubles. See [http://partsregistry.org/Part:BBa_B0015:Experience this] page.

Ethics

Ethics, bioethics and more ethics.

Modeling

Nick continued his succesful work on multicellularity in MatLab. He even created a graph that looks like the blueprints of some modern building + created bacteria that could go back in time ;)

We were also able to show the relative effect of the filter by outputting some graphs in MatLab.

Wiki

All parameters on the wiki AND in the MatLab model have been checked and should be correct.

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