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BYU 2014 Notebook Edit July August

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Alpha Amylase: Added DpnI to the PCR product for the digest of any plasmid that was not mutated properly and placed it in the 37 degree incubator. We will transform this digested plasmid into DH5a tomorrow. (JB)

30 June 2014

Alpha Amylase: Today the colony 8 PCR product for the Alpha Amylase mutant was transformed into DH5a using the basic transformation protocol as listed in the “Protocols” page. Tomorrow colonies with mutant Alpha Amylase pSB1C3 that survived the digest will be isolated and grown, then overnights can be made from these colonies for further work.

I also did some research for grants that we could apply for in order to receive more funding. Below are some links that may be useful to the team and others. (JB)

http://www.werf.org/i/Funding/Open_RFPs/a/o/rfp.aspx?hkey=05bda2a1-23af-4891-badf-815b2960d4f3

http://www2.epa.gov/education/environmental-education-ee-grants

http://www.nifa.usda.gov/fo/waterquality.cfm

https://experiment.com/start

Alpha Amylase: The previous transformation gave us several hundred colonies. This will make it difficult to find one that has the mutated Alpha Amylase plasmid. We will need to re-transform the PCR product into DH5a. (JB)

7 July 2014

Alpha Amylase: Dr. Grose said that the likely reason for no colonies was due to a diluted amount of PCR product being used since I only used 10 uL of the original mutated PCR product and added water, buffer, and DpnI for the digest I tried. She suggested transforming 10 uL of the PCR product + buffer mix in order to have a better chance of getting colonies with the mutated plasmid. (JB)

Alpha Amylase: Transformations yesterday do not appear to have worked. Desi said that we could take the previous plate where we got several hundred colonies, pick from single colonies, streak them on a plate to grow them up and make sure we can obtain single colonies since they were so small on the last plate, and run PCR on them to see if there are any that look like they have the plasmid in them. (JB)

Alpha Amylase: We discovered that the box of DH5a we had been using last week was not actually DH5a as someone had put the wrong tubes in the box. Hopefully this means that the transformations are working (given that we are actually transforming it into DH5a!). The mutated alpha amylase was retransformed into DH5a using 10 uL of PCR product as suggested last time by Dr. Grose since the PCR product was diluted during DpnI digest. (JB)

Alpha Amylase: Finally, it looks like we may have some progress coming. Despite accidentally spilling half of my transformation in the plating process. There was one colony, so it is looking more promising that the digest was effective and we may have one colony that was successfully mutated!

A liquid culture overnight in chloramphenicol was prepared from the single colony and the leftover on the stick was streaked on a chloramphenicol plate. A plasmid prep will be performed on the overnight and this will be sequenced in order to determine if this colony contains the mutant plasmid or the wild-type plasmid. (JB)

AiiA: Today I completed the ligation and transformation of Aii into DH5-alpha. Because my sequencing returned an empty backbone last time, I am hoping that it works this time around. I am planning on picking up the plates tomorrow to prepare for colony PCR. (CZ)