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//Preliminary Stages//

 We began our project by choosing the groups, doing preliminary research, and then beginning the DNA extraction of the lichen samples provided by the University of Connecticut (UConn). We knew when we began the project that it would require a lot of work, devotion, and numerous cycles of trial and error.





//29 April 2011//



Today we put the samples in the thermocycler so that it could undergo PCR. We also blasted the ITS regions on the website for National Center for Biotechnology Information.

//3 May 2011//

 After the weekend, we returned to the lab to discover that the PCR did not produce any bands. Therefore, we had to consider what steps we could take in order to ensure that we get results. Our game plan was to process more samples (DNA extraction) and then run the extracted DNA (5 samples) on a 1% agarose gel. We would be using 10 μL of 2 EZ vision with a 1 KB ladder.

 Initially, we used 1 μL of target, 1 μL Pf,1 μL Pr,12.5 μL MAST, 9.5 μL H2O, which amounts 25 μL total. In order to fix our results so that we produce bands, we used 2 μL target, 25 μL H2O (primer, master), 0.5 μL target, 1.0 μL each primer (master mix), and 10 μL H2O.



//4 May 2011//

 Today, we're preparing for our second run of PCR.

 Considering that the ITS region amounts to around 500 base pairs, we're running PCR on:

<span style="font-family: Georgia,serif;"> 1) Four 15 μL + 3 EZ [vision] samples of the extracted DNA on a 1% agarose gel with a 1KB ladder

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<span style="font-family: Georgia,serif;"> 2) 10 PCR samples on a 2% agarose gel which was run at 300 volts for 8 minutes using LB buffer. For the 2% agarose gel, we used 100 BP.

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<span style="font-family: Georgia,serif; font-size: 18px;">//6 May 2011//

<span style="font-family: Georgia,serif;">Lo and behold, we have results! We began preparing diluted samples of DNA for future PCR runs.

<span style="font-family: Georgia,serif; font-size: 18px;">//9 May 2011//

<span style="font-family: Georgia,serif;"> We ran the PCR. We made sure to consider the amount of DNA we extracted in order to ensure that we came up with results in the future.

<span style="font-family: Georgia,serif; font-size: 18px;">//10 May 2011//

<span style="font-family: Georgia,serif; margin: 0px; padding: 0px;">Our second round of results are in!

<span style="font-family: Georgia,serif;">Below is a list of the samples. The letters (A, B, C, D, etc.) represent different methods of preparing the samples (aka procedures for PCR)...
 * <span style="font-family: Georgia,serif;">Samples that have worked are in bold:

<span style="color: black; font-family: Georgia,serif; font-size: 10pt; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">1) C/D <span style="color: black; font-family: Georgia,serif; font-size: 10pt; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">2) C/D <span style="font-family: Georgia,serif; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">** 3) ** **B/C/D (2 microliter template of DNA)** <span style="color: black; font-family: Georgia,serif; font-size: 10pt; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">4) C/D <span style="color: black; font-family: Georgia,serif; font-size: 10pt; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">5) C/D <span style="color: black; font-family: Georgia,serif; font-size: 10pt; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">6) A/B <span style="font-family: Georgia,serif; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">** 7) D (10-2 dilution of DNA) ** <span style="font-family: Georgia,serif; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">** 8) D (10-2 dilution of DNA) ** <span style="font-family: Georgia,serif; line-height: 14.25pt; margin-bottom: 0in; margin-left: 0.5in; margin-right: 0in; margin-top: 0in; text-indent: -0.25in;">** 9) **<span style="color: black; font-family: Georgia,serif;">**C (10-1 dilution of DNA)**

<span style="font-family: Georgia,serif; font-size: 18px;">//11 May 2011//

<span style="font-family: Georgia,serif; margin: 0px; padding: 0px;">Today, we're diluting the extracted DNA and running a third gel.

<span style="font-family: Georgia,serif; font-size: 18px;">//13 May 2011//

<span style="font-family: Georgia,serif; margin: 0px; padding: 0px;">We're working on making our wiki manageable and readily accesible to all audiences (including parents)! As some students work on the website, others are working on the PCR samples and on gel electrophoresis. Although it's Friday the 13th, we are not expecting any misfortune. After all, this is varsity!

<span style="font-family: Georgia,serif; font-size: 18px;">//14 May 2011//

<span style="font-family: Georgia,serif;">Happy Saturday, all!

<span style="font-family: Georgia,serif;">Today, we're finishing our work on the PCR gels so that we can get them all run. Others are working on a separate assignment titled "paper genetic engineering" where they are getting a feel for an extremely important topic in genetics aside from DNA barcoding. The exercise, which involves carefully analyzing strands of paper DNA and cutting and reattaching them in various places, will simulate the steps one would need to carry out if he or she was to isolate and insert a particular gene into a different organism; in other words, genetically engineer or modify the recipient.

<span style="font-family: Georgia,serif; margin: 0px; padding: 0px;">It's been a busy week but we're getting some good results as well as excellent feedback.

<span style="font-family: Georgia,serif; margin: 0px; padding: 0px;">Speaking of feedback, check out our wiki stats as of 14 May 2011! Not only is there a lot of work being done, but visitors are starting to come in!

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<span style="font-family: Georgia,serif;"> Here are some Saturday photos!

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<span style="font-family: Georgia,serif; font-size: 18px;">//17 May 2011//

<span style="margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px; padding-bottom: 0px; padding-left: 0px; padding-right: 0px; padding-top: 0px;"><span style="font-family: Georgia,serif;">While one group is extracting DNA, another group is prepping more agarose gels. Others continue their work on the paper genetic engineering assignment.

<span style="font-family: Georgia,serif;">__ Links: __

<span style="display: block; font-family: arial,helvetica,sans-serif; font-size: 13px; font-style: normal; font-weight: normal; line-height: 19px; text-align: center;"><span style="font-family: Georgia,serif;">//**__ T2 HOME __**// <span style="display: block; font-family: arial,helvetica,sans-serif; font-size: 13px; font-style: normal; font-weight: normal; line-height: 19px; text-align: center;"> <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">Responsibilities  <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"> <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">Procedure  <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">Lichen Background  <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">PCR Background  <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">Background on DNA Barcoding  <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="background-attachment: initial; background-clip: initial; background-color: initial; background-origin: initial; background-position: 100% 50%; background-repeat: no-repeat no-repeat; cursor: pointer; padding-right: 10px;">Electrophoresis   <span style="cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; font-style: normal; font-weight: normal; line-height: 30px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif; font-size: 20px; line-height: 30px;">Results  <span style="background-position: 100% 50%; cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; line-height: 30px; padding-right: 10px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">T2 (B)Log  <span style="background-position: 100% 50%; cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; line-height: 30px; padding-right: 10px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">@T2 Resources  <span style="background-position: 100% 50%; cursor: pointer; display: block; font-family: Georgia,serif; font-size: 20px; line-height: 30px; padding-right: 10px; text-align: center;"><span style="cursor: pointer; font-family: Georgia,serif;">T2 Visitors