Team:Nevada/iGEMcollaborators

From 2011.igem.org

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Revision as of 23:24, 28 September 2011

Contribution to the pSB1C3 The iGEM team Nevada contributed with correction of pSB1C3. Megan Tabor detected the error in the pSB1C3(the chloramphenicol resistant backbone). pSB1C3 is the submission plasmid for iGEM and we were also using it for our our thiamnie knockout construct that will make the Synacasistis an auxotrouph. When trying to make the primers for isolation of the chloramphenical resistance protein from the plasmid using PCR, the mapped out section did not blast as chlormamphenical resistance and did not fit with the ORF. Megan contacted the MIT team that created the pSB1C3 to find more information and a correction. Below are the emails of the conversation.

From: Megan Tabor <tabormi22@gmail.com> Date: Mon, Aug 1, 2011 at 4:53 PM Subject: iGEM Team Nevada 2011 To: webmail@austinche.name

Hello Austin,

My name is Megan Tabor and I am a currant iGEM member. I am trying to work with the plasmid backbone pSB1C3 ( the chloramphenicol resistant backbone). I would like to isolate it out of the plasmid but there does not seem to be a start or stop codon associated with where on the plasmid the resistance is supposed to be. I was wondering if you know for sure that is resistance is where it was stated. Thank you so much for your time.
Megan Tabor
Forwarded message -------------------
From: Austin Che <austin@csail.mit.edu>
Date: Tue, Aug 2, 2011 at 6:06 AM
Subject: Re: iGEM Team Nevada 2011
To: Megan Tabor <tabormi22@gmail.com>

The annotation on the registry was off by 2 bases on either side. I've updated the registry info.
Hello Dr Knight,
My name is Megan Tabor. I am a current member of iGEM and I am trying to isolate the chloramphenicol resistance out of pSB1C3. I have put the sequence through BLAST and nothing CmR matches. I also do not notice a start or stop codon around the CmR. I was wondering if it is known that the CmR is where it is stated on the sequence, and where does it start transcribing. Thank you so much for your time.
Megan Tabor Aug 1

The CmR gene is oriented in the reverse direction, so you probably are missing the start/stop codons. You can find the genes using the ORF Finder, part of the NCBI program. Copy and paste the sequence into the window on the the orf finder page (http://ncbi.nlm.nih.gov/gorf). The gene is located in the bottom frame, and if you select that frame and click "blast" you will get matches of the gene in Genbank.
I believe there is already a CmR part in the registry, P1000.

@@ Line 4: / Line 4: @@
-<p>From: Megan Tabor <tabormi22@gmail.com>
+From: Megan Tabor <tabormi22@gmail.com>
 Date: Mon, Aug 1, 2011 at 4:53 PM
 Subject: iGEM Team Nevada 2011
@@ Line 19: / Line 19: @@
 ---------- Forwarded message -------------------
 From: Austin Che <austin@csail.mit.edu>
 Date: Tue, Aug 2, 2011 at 6:06 AM
 Subject: Re: iGEM Team Nevada 2011
 To: Megan Tabor <tabormi22@gmail.com>
@@ Line 28: / Line 31: @@
   side. I've updated the registry info.
-Hello Dr Knight,<p>
+Hello Dr Knight,
 My name is Megan Tabor.  I am a current member of iGEM and I am trying to isolate the chloramphenicol resistance out of pSB1C3.  I have put the sequence through BLAST and nothing CmR matches.  I also do not notice a start or stop codon around the CmR.  I was wondering if it is known that the CmR is where it is stated on the sequence, and where does it start transcribing. Thank you so much for your time.