Katpak:m1d1

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Module 1 Day 1: Start-up genome engineering
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1. Generate a table that lists each gene and any re-engineering ideas you have for it.

2. Nature often preserves functionally critical genomic elements, and evolutionary cousins can help us identify which genetic elements are disposable, which are interchangeable, and which are essential. Who are M13's closest evolutionary relatives and how do they differ from the phage you're working with? M13's closest evolutionary cousins are the other small, filamentous, male-specific coliphages--fd and f1. These phages are characterized by a small, single-stranded circular DNA genome of about 6400 bases. There is an average of 3.0% of nucleotide-sequence differences between the M13 and fd genomes. Only 12 of the changes result in change of amino acids. M13 DNA is only a single nucleotide shorter than fd DNA.

3. Look up part BBa_M1307 and write a response to the following criticism: "BBa_M1307 is not a standard biological part and does not belong in the registry. BBa_M1307 is the M13K07 genome with an addition of pACYC177 bearing the p15a bacterial origin of replication and a kanamycin resistance gene. As defined in lecture, a part is a basic biological function that can be encoded by as genetic material. The sequence of BBa_M1307 encodes multiple function (infection, replication of phage genome, assembly of phage proteins, kanamycin resistance, etc) and thus is not by definition a standard biological part. It is more of a device, defined as a combination of one or more parts that provide a human-defined function. Still, it seems that this very basic-level sequence is necessary regardless of the name we give it because it is a starting-point for engineering of the M13 genome. Thus, even if BBa_M1307 does not belong under a "parts" category, it should still be available as a sequence in the registry.