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Metagenomics

Please provide some assistance in answering the following questions:

1. Why do we use 16s rDNA for sequencing?
2. Why do we use the nanodrop on our DNA extracts?
3. How does PCR work, and why did we need to PCR the DNA extracts?
4. What does the agarose gel run tell us about our PCR products?

Solution Preview

1. In metagenomics, the challenge often lies in identifying microorganisms which are highly a like in many ways except in rDNA expression. As a result, 16s rDNA sequencing helps us more accurately determine the species make up of a sample that has been collected. For reference, this article actually goes into detail about some of the discoveries 16s rDNA sequencing has granted which otherwise would have been difficult or impossible:

Reference: http://www.ncbi.nlm.nih.gov/pubmed/18828852

2. The nanodrop, I presume is the 'NanoDrop Microvolume Quantification device'. It measures the concentration of nucleic acid in a liquid sample. We do this in order to standardize how much nucleic acid we are putting into, say, PCR for amplification. This ...

Solution Summary

Why we use 16s rDNA for sequencing is determined. Nanodrop on our DNA extracts are also determined.

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