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Team:The University of Alberta/16 May 2008
From 2008.igem.org
To Do
Plant Seminar @ 4:00pm
In the Lab
Chris
- I finished sequencing the thiolase gene again; the samples need to be run up to the MBSU
- Jason and I designed the BioBrick for PIF3; I spent some time trying to do codon optimization for E.Coli
I downloaded a program onto one of the computers in the back of the lab for optimizing the BioBricks but it doesnt seem to work very well; use this[http://genomes.urv.es/OPTIMIZER] website instead if you want to work on codon optimization.
- The PIF3 BioBrick doesn't have a His-tag added to it. Can't forget to do that before we get them synthesized.
If anyone wants to work on building BioBricks, these sites are a good help:
- http://www.arabidopsis.org - The Arabidposis Information Resource (TAIR): This site will help you find the sequences for the genes and proteins that we want from Arabidopsis. It's best if you use cDNA sequences because these already have the introns spliced from them!
- http://www.ebi.ac.uk/Tools/clustalw2/index.html - ClustalW: This site is great for aligning two DNA or protein sequences. This makes it super easy to check to make sure your edited/optimized sequences still code from the same thing as the reference sequences from TAIR.
- http://www.expasy.ch/ - ExPASy Proteomics Server: This site has tons of tools that we'll probably never use, but there are still a few useful things:
- Translate(http://www.expasy.ch/tools/dna.html) This will let you translate your cDNA sequence into an amino acid sequence at the click of a button!
- ProSite and ScanProSite (http://www.expasy.ch/prosite/) These let you search your amino acid sequence to check for domains, modification sites, etc. Probably not useful but it does have a tool that allows you to make some neat schematic diagrams of genes/proteins like the one below:
Jason
- I also started working on the Phytochromobilin operon this involved finding the sequences and removing all useless DNA (utr, introns etc.)This operon does not have a his tag added yet either.
- Me and James where thinking of using I0500 as the vector for our constructs as it has an arabinose induced promoter that would allow us to control transcription if these genes turn out to be toxic. If it turns out these genes are not toxic we might then start thinking of moving them into a plasmid with a constituative promoter. Lab Tip of the Day Tweezers can be sharp and sometime break the skin if fiddled with. One should use the upmost caution when handling and always read the manual and wear proper PPE when handling.
