T3+Journal

__**Tuesday, April 26, 2011**__ We instigated our research, delegated the groups, and began the DNA extraction of our Lichen samples provided by the University of Connecticut.

Errors in the extraction process:
 * Sample 26 -- had to regrind lichen after the PL1 and RNase A were added because the sample was not originally ground enough
 * Sample 28 -- had to regrind lichen after the PL1 was added because the sample was not originally ground enough
 * Sample 29 -- the pipette was not set to 400 µL for PL1. it was set to 340 µL so 40 µL was added.
 * Sample 30 -- same error as sample 28



__**Friday, April 29, 2011**__ One group homogenized samples 31,32,33,34,36,37,38,40,41,46,47,48 to reduce errors of grinding issues for the next extractions. Another resuspended primers for samples 26-30 while the Thermocycle was set for the PCR. The samples did not go in during our class though because the other section was also doing the PCR today. It made sense for the samples to go into the Thermocycle together.

__**Monday, May 2, 2011**__ We did Electrophoresis for samples 26-30. The order of the gel was as such: Ladder / 26 / 27 / 28 / 29 / 30 / Ladder. For results, only lanes 4 and 5 ( 28 / 29) had faint DNA bands show up. The two possible reasons for the faint bands in the lanes of samples 28 / 29 and empty lanes 26 / 27 / 30 are that was too much or not enough template DNA. We planned to run an electrophoresis gel the following day for the extracted DNA and to alter the PCR procedure.\



__**Tuesday, May 3, 2011**__ We went back to our original extracted DNA to ensure that the extraction of samples 26 - 30 was successfully performed. Unfortunately, no bands appeared on the gel, thus we could not disprove either theory that the DNA was too concentrated or too diluted. We extracted samples 31 - 34 to set up for another electrophoresis which would verify that DNA was in fact extracted from the samples.

We diluted the extracted DNA 31 - 34 to see if the electrophoresis problem was the DNA concentration. After performing these dilutions, we ran them through the original PCR procedure.
 * __Thursday, May 5, 201____1__**

__**Friday, May 6, 2011**__ Took dilutions that had been run through the PCR, and prepared them for electrophoresis. After running the electrophoresis, the results were as follows: NOTHING! This information leads us to believe that there is something wrong with our extraction procedure.

we re-extracted samples 26-34 and began extracting 35-41. this time around we incubated for 60 minutes as a way to insure the cells were rupturing. we had a primer accident, the water was added to the stock of the primers instead of to a dilution tube, we were able to salvage this mistake by halving the original concentration of the primers.
 * __Monday, May 9, 2011__**

Today we continue to find the right dilution for our DNA extraction. Finished the elution (using a different buffer) of 26-41. the PCR was prepared for the samples as well as the dilution.
 * __Tuesday, May 10, 2011__**



__**Thursday, May 12, 2011**__ Today we continued work on our 4th dilution, as well as begin a packet on genetic engineering to further expound our knowledge on the subject. after the dilutions they will be put in PCR and then the thermo-cycler. the gels were prepared for Friday.





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