Spenser Skates: Genome Engineering Day 1

1. The major writing assignment for this module will be a description of your M13 renovation work. Use the summary in your lab notebook to start a table on your wiki user page to organize your thoughts about the existing genome. 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 have the following virus classifiction: Familia: Inoviridae Genus: Inovirus Species: Enterobacteria phage M13 The M13 virus is most closely related to f1 and d1 bacteriophage. These have about a 3% difference in base pair sequence. M13 is different from other closely related bacteriophages in its lysogenic life cycle. 3. Register for an account at the Registry for Standard Biological Parts. This site is a clearing house for engineered biological parts that can be used as substrates for building. 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 a bacterial origin of replication and a kanamycin resistance gene. A "part" is a basic funciton encoded by genetic material. BBa_M1307 is significantly larger than a standard part as it encodes instructions for all of the M13 bacteriophage lifecycle. It is better considered as a device, which performs some defined function, in this case continual infection of Ecoli cells. However, it is still useful because it does encode multiple biological parts within the genome. Furthermore, much of the knowledge of the function of individual parts is lost without an understanding of the interaction between parts and the rest of the M13 genome, which is essential for each of the individual parts' function.