SDU-Denmark/9 July 2010
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+ | '''Phototaxis:''' | ||
+ | <br>''progress report:'' We have run colony-PCR on the cambridge BBa_K274210 brick we have attempted to transform into our cells. We have also run colony pcr on a RBS, a RFP reporter and a heat inducible promoter. All but the K274210 colonies showed bands at correct lengths, and the RFP colonies had turned bright red. | ||
+ | <br>Jakob has ordered primers and cDNA from drosophila melanogaster. | ||
+ | <br>Lars Christian and Maria will be working over the weekend, to make overnight cultures, and freeze cells, so we will be ready to make a new batch of competent cells next week. We need both coli TOP10 and M1655. | ||
+ | <br><br>Troubleshooting on Cambridge brick: | ||
+ | <Br>We suspect our elongation time of being to short. This might explain the smear at the bottom of each well. | ||
+ | <Br>-The length of the part in this plasmid is 4856Bp. | ||
+ | <br>-The reaction rate for this enzyme is stated as 35-100nt/sec at 72°C and 40% of that at 55°C | ||
+ | <br>-we ran the elongation for 5 minutes at 55°C giving us 4200-12.000 nt/elongation. | ||
+ | <br><br>Another problem could be the length of our part. Apparently we are opperating on the limit of what the polymerase can do, most companies stating that it will work for 3-4kb and can be pressed to 5kb if conditions are optimal. Many also suggest increasing [MgCl2] at low yields. We might also attempt that. Yet another possibility is that our colonies didn't contain any plasmids with our part. | ||
+ | <br><br>We will be attempting new colony pcr in the coming week, with elongation set to at least 6 minutes at 55°C. Perhaps we will attempt it with two different polymerases, increasing [MgCl2] in the Taq mix. | ||
+ | <Br><br>We have considered other ways of getting physical dna for our fusion protein. Two options come to mind if we can't get it from spudich lab. | ||
+ | <br>- getting it synthesized | ||
+ | <br>- Maybe getting the strain with the natromonas proteins from the 2007 melbourne team. | ||
+ | <br><br>''working hypothosis'': No changes | ||
+ | <br><br>--[[User:CKurtzhals|CKurtzhals]] 21:23, 9 July 2010 (UTC) | ||
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'''Flagella''' | '''Flagella''' | ||
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--[[User:Louch07|Louch07]] 16:00, 9 July 2010 (UTC) | --[[User:Louch07|Louch07]] 16:00, 9 July 2010 (UTC) | ||
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+ | '''Modelling''' | ||
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+ | ''Progress report:'' We have started implementing our model. We are discussing which forces are actually effecting the system. Besides the forces produced by the flagellas, we are discussing whether the flagellas have a favored position that it would be pushed towards, when not effected by outer forces. We are also discussing whether thermal forces should be included. | ||
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+ | ''Working Hypothesis:'' No Change. |
Latest revision as of 12:29, 16 July 2010