Hey Nate, I thought what you had was a good presentation! But one thing I was wondering was why you were testing 2 microliter and 3 microliters for your gel. Although I know it was for quality control, I was a bit lost about the significance between those quantifiable difference. If you could let me know about what those mean for your experiment I think that would help me. Thanks!
Hey Rampy, I thought your experiment turned out great! I was just wondering what the significance between your microliters was for your quality control. I would like to have a better idea why size matters for this experiment to determine the quality of your samples. Thanks!
To determine the phage cluster, first a restriction digest would be done on the phage DNA. This involves separately introducing enzymes to the DNA that cut each DNA sample at points of the DNA. The cut DNA would be run on a gel to show “bands” based on the mass and length of the DNA pieces. The results would be entered into a website that compares the bands to those of other phage species. Indirectly, you could make a prediction of your own specie’s cluster by its similarity to previously known clusters’ phages. Because phage clusters are genomic groupings, a restriction digest could only allow you to make a prediction of cluster. I only mention restriction digest because it was the next step in our procedure (ours failed). Genomic sequencing is the only way to prove phage cluster.
The negative control was the empty space to the right of the bands. Because the bands were so visibly defined, it was assumed that they were satisfactory. Otherwise, there would have been streaks or cloudiness within the rest of the lane. I also forgot to add that the two lanes were labelled 2 microliters and 3 microliters to denote that two different volumes of the DNA solution were put in the gel lanes. Because there was no difference, the concentration of the DNA solution was high enough to stay similarly bright between the two lanes.
curesymposium.org 
Hey Nate, I thought what you had was a good presentation! But one thing I was wondering was why you were testing 2 microliter and 3 microliters for your gel. Although I know it was for quality control, I was a bit lost about the significance between those quantifiable difference. If you could let me know about what those mean for your experiment I think that would help me. Thanks!
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Hey Rampy, I thought your experiment turned out great! I was just wondering what the significance between your microliters was for your quality control. I would like to have a better idea why size matters for this experiment to determine the quality of your samples. Thanks!
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Hi, thank you. My response to Peter Kubiniec’s comment will hopefully answer your concern.
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Hi, thank you. My reply to Peter Kubiniec, below, hopefully answers your concern.
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What experiments would you perform to determine the phage cluster of GardenBox?
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To determine the phage cluster, first a restriction digest would be done on the phage DNA. This involves separately introducing enzymes to the DNA that cut each DNA sample at points of the DNA. The cut DNA would be run on a gel to show “bands” based on the mass and length of the DNA pieces. The results would be entered into a website that compares the bands to those of other phage species. Indirectly, you could make a prediction of your own specie’s cluster by its similarity to previously known clusters’ phages. Because phage clusters are genomic groupings, a restriction digest could only allow you to make a prediction of cluster. I only mention restriction digest because it was the next step in our procedure (ours failed). Genomic sequencing is the only way to prove phage cluster.
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How do you know the bands are clear enough to indicate that it can be used, did you test it against controls?
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The negative control was the empty space to the right of the bands. Because the bands were so visibly defined, it was assumed that they were satisfactory. Otherwise, there would have been streaks or cloudiness within the rest of the lane. I also forgot to add that the two lanes were labelled 2 microliters and 3 microliters to denote that two different volumes of the DNA solution were put in the gel lanes. Because there was no difference, the concentration of the DNA solution was high enough to stay similarly bright between the two lanes.
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