Team:Groningen/Notebook/2 July 2009

From 2009.igem.org

Wet

Yesterday we did a restriction digest (.5ug digested with 1U enzyme) on pBAD-HmtA (AgeI and PstI) and on pUC19 (PvuI), and tested the BioBrick gvp construct and terminator by PCR(protocol Quality Control iGEM 2008).

Contents of the gel:

1. =empty
2. =1kb marker (Fermentas)
3. =T1 (expected size...)

etc..

Conclusion:

• PCR products were too large, maybe one of the primers had gone bad...

Or the construct is not correct..

• Restriction fragments were ok, only PvuI did not completely cut pUC19 as there is an extra band with the size of single cut plasmid.

Dry

We looked at computing the volume of a gas vesicle based on its width and diameter, mostly based on Walsby1994. The results were not completely consistent with some of the values given in the text (we got 2.38... while the text said it was 2.35...), but that could have been due to intermediate rounding (by the authors of the text) and/or slightly different assumptions about the geometry of the vesicle, whose cross-section we assume looks like:

The results of our computations can be found on the vesicle project page. Furthermore, the protein sequences of "our" gvpA/B were run (by Nienke) through [http://blast.ncbi.nlm.nih.gov/Blast.cgi Blast] to compare them with other gvpA/B proteins. Two matches were found with the Anabaena gvpA/B protein, both with no gaps, 73%/74% "identities" and 95% "positives" (there were also lots of other matches with gvpA/B proteins from other bacteria). This is apparently quite a good match, so we proceed on the assumption that most of the general data on the physical properties of the gas vesicles we found in Walsby1994 applies to our case.